Variant report

Variant	rs34254874
Chromosome Location	chr10:953874-953875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:953469-953915	K562	blood:	n/a	n/a
2	POLR2A	chr10:953652-953927	GM12891	blood:	n/a	n/a
3	POLR2A	chr10:947200-954920	K562	blood:	n/a	n/a
4	POLR2A	chr10:953633-953925	K562	blood:	n/a	n/a
5	POLR2A	chr10:953868-954100	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:953733-953931	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:953309-954590	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr10:953740-953877	K562	blood:	n/a	n/a
9	POLR2A	chr10:953597-953916	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:953280..955249-chr10:957208..959936,2	MCF-7	breast:
2	chr10:953256..955911-chr10:1033509..1036412,2	K562	blood:
3	chr10:947556..951451-chr10:951605..956878,5	K562	blood:
4	chr10:951945..954088-chr10:957080..959590,3	MCF-7	breast:

Variant related genes	Relation type
LARP4B	TF binding region
ENSG00000107937	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000205740	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1013505	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508208	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904577	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904580	1.00[ASN][1000 genomes]
rs10904581	1.00[ASN][1000 genomes]
rs10904583	1.00[ASN][1000 genomes]
rs10904584	1.00[ASN][1000 genomes]
rs1106064	1.00[ASN][1000 genomes]
rs11253458	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253459	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11253460	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253462	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11253465	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11253467	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253468	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253473	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253475	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253485	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253488	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253492	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253493	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253494	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253495	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11253499	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253509	1.00[ASN][1000 genomes]
rs11253511	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11253513	1.00[ASN][1000 genomes]
rs11253517	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11253520	1.00[ASN][1000 genomes]
rs11253521	1.00[ASN][1000 genomes]
rs11812170	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812523	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813210	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11815185	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11816064	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817793	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11818288	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11818325	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12240651	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244253	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244355	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249634	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249828	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250936	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250937	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251396	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12254002	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258388	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259338	1.00[ASN][1000 genomes]
rs12259720	1.00[ASN][1000 genomes]
rs12259801	1.00[ASN][1000 genomes]
rs12260800	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261911	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12264390	1.00[ASN][1000 genomes]
rs12264711	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12267709	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354639	1.00[ASN][1000 genomes]
rs12359645	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12360270	1.00[ASN][1000 genomes]
rs12761424	1.00[ASN][1000 genomes]
rs12762973	1.00[ASN][1000 genomes]
rs12763396	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12764024	1.00[ASN][1000 genomes]
rs12765174	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766381	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12769431	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12769873	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770190	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778891	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783472	1.00[ASN][1000 genomes]
rs13377166	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341741	0.80[AMR][1000 genomes]
rs1341742	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1539174	1.00[ASN][1000 genomes]
rs1555899	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159950	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159970	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050944	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270014	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34284130	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405399	1.00[ASN][1000 genomes]
rs34433840	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34847097	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35174953	1.00[ASN][1000 genomes]
rs35394603	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35567307	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35637113	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35693858	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35825568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968821	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522091	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56318703	1.00[ASN][1000 genomes]
rs56347655	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61830929	1.00[ASN][1000 genomes]
rs61830932	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66631678	0.84[AMR][1000 genomes]
rs7067865	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074642	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077278	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778215	0.84[AMR][1000 genomes]
rs72778229	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765867	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908138	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:852200-956400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:870600-959400	Weak transcription	Stomach Mucosa	stomach
3	chr10:927600-972600	Weak transcription	Hela-S3	cervix
4	chr10:928000-954200	Weak transcription	Brain Germinal Matrix	brain
5	chr10:928000-954200	Weak transcription	Fetal Brain Female	brain
6	chr10:928000-963200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:928000-966400	Weak transcription	Small Intestine	intestine
8	chr10:929400-955800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:929400-975800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:929400-976400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:929800-954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:930000-954400	Weak transcription	Colonic Mucosa	Colon
13	chr10:931400-956000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr10:931600-965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:931600-967400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:931800-954000	Weak transcription	Thymus	Thymus
17	chr10:931800-954200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:931800-957600	Weak transcription	Aorta	Aorta
19	chr10:932200-955800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr10:935400-964000	Weak transcription	Psoas Muscle	Psoas
21	chr10:940000-970200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:940200-967600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:940400-955800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:942200-954000	Weak transcription	Ovary	ovary
25	chr10:943400-954200	Weak transcription	Liver	Liver
26	chr10:944600-956200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:945200-954200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:946000-965400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr10:946000-966600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr10:946200-956200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:946200-965400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr10:946600-955400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:947200-955000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:947200-958400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:947800-954000	Weak transcription	Fetal Lung	lung
36	chr10:947800-956200	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:947800-975400	Weak transcription	Fetal Brain Male	brain
38	chr10:948400-954200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr10:948400-955400	Weak transcription	HSMMtube	muscle
40	chr10:948800-958600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr10:949000-954600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:949000-959800	Strong transcription	Dnd41	blood
43	chr10:949600-954000	Weak transcription	Esophagus	oesophagus
44	chr10:949600-954000	Weak transcription	HSMM	muscle
45	chr10:949600-955600	Weak transcription	Fetal Heart	heart
46	chr10:949600-959000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr10:949600-965400	Weak transcription	Right Ventricle	heart
48	chr10:949600-974600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr10:949800-954200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr10:949800-954200	Weak transcription	HUVEC	blood vessel

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