Variant report

Variant	rs11253517
Chromosome Location	chr10:970524-970525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:949318..951166-chr10:969815..971426,2	MCF-7	breast:
2	chr10:968239..971005-chr10:1062615..1065271,2	MCF-7	breast:
3	chr10:969783..971974-chr10:1038430..1041356,2	K562	blood:
4	chr10:968856..970673-chr10:1033223..1035399,2	K562	blood:
5	chr10:969504..972308-chr10:1100615..1103813,3	MCF-7	breast:
6	chr10:967396..974147-chr10:1032852..1035834,6	MCF-7	breast:
7	chr10:950294..953048-chr10:969646..972009,2	K562	blood:

Variant related genes	Relation type
ENSG00000107929	Chromatin interaction
ENSG00000205740	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000107937	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1013505	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs10508208	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs10904577	1.00[ASN][1000 genomes]
rs10904580	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904581	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904583	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904584	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106064	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253444	0.89[CEU][hapmap]
rs11253445	0.89[CEU][hapmap]
rs11253446	0.89[CEU][hapmap]
rs11253458	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253459	0.88[CEU][hapmap]
rs11253460	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253465	1.00[ASN][1000 genomes]
rs11253467	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs11253468	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253473	1.00[ASN][1000 genomes]
rs11253475	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253485	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253488	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253492	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253493	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11253494	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs11253495	0.94[CEU][hapmap]
rs11253499	1.00[ASN][1000 genomes]
rs11253504	0.88[CEU][hapmap]
rs11253509	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253511	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253513	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253520	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253521	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253540	0.89[MKK][hapmap]
rs11253560	0.89[MKK][hapmap]
rs11812170	1.00[ASN][1000 genomes]
rs11812523	1.00[ASN][1000 genomes]
rs11813210	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11815185	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11816064	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11817793	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs11818288	1.00[ASN][1000 genomes]
rs11818325	1.00[ASN][1000 genomes]
rs12240651	1.00[ASN][1000 genomes]
rs12244253	1.00[ASN][1000 genomes]
rs12244355	1.00[ASN][1000 genomes]
rs12249634	1.00[ASN][1000 genomes]
rs12249828	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs12250936	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12250937	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12251396	1.00[ASN][1000 genomes]
rs12254002	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs12258388	1.00[ASN][1000 genomes]
rs12259338	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259720	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259801	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260800	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs12261911	1.00[ASN][1000 genomes]
rs12264390	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264711	1.00[ASN][1000 genomes]
rs12267709	1.00[ASN][1000 genomes]
rs12354639	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	0.89[CEU][hapmap]
rs12359645	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761424	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12762973	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12763396	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12764024	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs12765174	1.00[ASN][1000 genomes]
rs12766381	1.00[ASN][1000 genomes]
rs12768348	0.89[CEU][hapmap]
rs12769002	0.89[CEU][hapmap]
rs12769431	1.00[ASN][1000 genomes]
rs12769873	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs12770190	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs12772979	0.89[MKK][hapmap]
rs12774985	0.89[CEU][hapmap]
rs12778891	1.00[ASN][1000 genomes]
rs12783472	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377166	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs1341741	0.94[CEU][hapmap];1.00[GIH][hapmap]
rs1341742	1.00[ASN][1000 genomes]
rs1539174	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555899	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159950	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs17159970	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs17221491	0.84[MKK][hapmap]
rs17293608	0.89[MKK][hapmap]
rs2050944	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs34254874	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34270014	1.00[ASN][1000 genomes]
rs34284130	1.00[ASN][1000 genomes]
rs34405399	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433840	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34847097	1.00[ASN][1000 genomes]
rs35174953	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35394603	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35567307	1.00[ASN][1000 genomes]
rs35637113	1.00[ASN][1000 genomes]
rs35693858	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825568	1.00[ASN][1000 genomes]
rs35968821	1.00[ASN][1000 genomes]
rs4522091	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs56318703	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347655	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61830929	1.00[ASN][1000 genomes]
rs61830932	1.00[ASN][1000 genomes]
rs7067865	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7074642	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7077278	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs72778229	1.00[ASN][1000 genomes]
rs765867	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs7908138	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914758	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv825207	chr10:957020-1005451	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
18	nsv825208	chr10:965883-1004836	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11253517	DIP2C	cis	cerebellum	SCAN
rs11253517	GTPBP4	cis	lymphoblastoid	seeQTL
rs11253517	PFKP	cis	parietal	SCAN
rs11253517	ADARB2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:927600-972600	Weak transcription	Hela-S3	cervix
2	chr10:929400-975800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:929400-976400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:947800-975400	Weak transcription	Fetal Brain Male	brain
5	chr10:949600-974600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:951000-975400	Weak transcription	Fetal Kidney	kidney
7	chr10:952600-971000	Weak transcription	Brain Substantia Nigra	brain
8	chr10:952600-975400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:953000-974400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:954600-975000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr10:954800-973600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:955000-974600	Weak transcription	Colonic Mucosa	Colon
13	chr10:956200-972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:956800-975400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:956800-975600	Weak transcription	Fetal Brain Female	brain
16	chr10:956800-976400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:957000-970600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:957600-975200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:958000-972000	Weak transcription	HUVEC	blood vessel
20	chr10:958000-972600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr10:958000-975600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr10:958200-974000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:958200-974200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:959400-973200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:964200-970600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr10:965800-976200	Weak transcription	Aorta	Aorta
27	chr10:966000-971000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr10:966200-972000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:966200-975000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:966800-974400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr10:967000-972600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:967400-970600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr10:967400-972400	Strong transcription	Dnd41	blood
34	chr10:967400-973200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:967600-971200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr10:967600-972800	Strong transcription	Fetal Thymus	thymus
37	chr10:968000-970600	Weak transcription	Liver	Liver
38	chr10:968000-970600	Strong transcription	Fetal Intestine Small	intestine
39	chr10:968000-971200	Strong transcription	Fetal Intestine Large	intestine
40	chr10:968000-972400	Weak transcription	Esophagus	oesophagus
41	chr10:968000-973000	Strong transcription	Fetal Stomach	stomach
42	chr10:968000-973600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:968000-974400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:968000-975800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr10:968200-972000	Weak transcription	Fetal Lung	lung
46	chr10:968200-972600	Strong transcription	Primary B cells from cord blood	blood
47	chr10:968200-974200	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:968400-970600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:968400-970600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr10:968400-970600	Weak transcription	Placenta	Placenta

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