Variant report

Variant	rs11250242
Chromosome Location	chr10:1100064-1100065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr10:1100039-1100094	K562	blood:	n/a	n/a
2	POLR2A	chr10:1099971-1103106	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr10:1100038-1100578	HepG2	liver:	n/a	n/a
4	POLR2A	chr10:1099824-1100550	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:1099924-1103110	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1032122..1034803-chr10:1098980..1100497,2	MCF-7	breast:
2	chr10:833990..835898-chr10:1099433..1102164,2	K562	blood:
3	chr10:1031887..1035944-chr10:1099515..1103666,8	MCF-7	breast:
4	chr10:1090197..1098635-chr10:1098667..1108160,39	K562	blood:
5	chr10:1024931..1026734-chr10:1099565..1101968,2	MCF-7	breast:
6	chr10:975799..978442-chr10:1098842..1102725,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IDI1-2	chr10:1099888-1100616	NONHSAT010896
2	lnc-IDI1-2	chr10:1099766-1100185	NONHSAT010897

No data

Variant related genes	Relation type
WDR37	TF binding region
IDI1	TF binding region
ENSG00000067064	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000205740	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000107937	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10047269	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047382	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10047383	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10219038	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044261	0.85[CEU][hapmap]
rs1079389	0.88[EUR][1000 genomes]
rs1079390	0.88[EUR][1000 genomes]
rs10794720	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[EUR][1000 genomes]
rs11250249	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11250252	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11250264	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11815047	0.90[ASN][1000 genomes]
rs11816485	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11818314	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11819178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11819230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12241632	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap]
rs12247779	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12247818	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12250141	0.84[EUR][1000 genomes]
rs12268949	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359250	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[ASN][1000 genomes]
rs13377037	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap]
rs17155821	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap]
rs17155886	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2279256	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2387299	0.88[EUR][1000 genomes]
rs2892254	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3793776	0.90[CHB][hapmap];0.82[MEX][hapmap]
rs3793780	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs3793781	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs3886474	0.88[EUR][1000 genomes]
rs41299206	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56004802	0.88[EUR][1000 genomes]
rs57514701	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59377495	0.88[EUR][1000 genomes]
rs61571350	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7071670	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075830	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7093915	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100114	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117685	0.96[EUR][1000 genomes]
rs74117831	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74117848	0.88[EUR][1000 genomes]
rs74117849	0.88[EUR][1000 genomes]
rs74117850	0.88[EUR][1000 genomes]
rs74120451	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7922760	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
20	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv5532	chr10:1079499-1101700	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11250242	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1095800-1102000	Weak transcription	Spleen	Spleen
2	chr10:1096000-1101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:1096000-1101800	Weak transcription	Gastric	stomach
4	chr10:1096200-1100800	Weak transcription	Aorta	Aorta
5	chr10:1096800-1100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:1096800-1100200	Strong transcription	Fetal Muscle Leg	muscle
7	chr10:1096800-1100400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:1096800-1100600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr10:1096800-1100800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr10:1096800-1100800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:1096800-1100800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:1096800-1100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:1096800-1100800	Strong transcription	Fetal Thymus	thymus
14	chr10:1096800-1100800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr10:1096800-1100800	Weak transcription	Right Atrium	heart
16	chr10:1096800-1100800	Weak transcription	Small Intestine	intestine
17	chr10:1096800-1101600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:1096800-1101800	Weak transcription	Esophagus	oesophagus
19	chr10:1097000-1100200	Weak transcription	Colon Smooth Muscle	Colon
20	chr10:1097200-1100200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:1097200-1100200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:1097200-1100600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:1097200-1100600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:1097200-1100600	Strong transcription	Placenta	Placenta
25	chr10:1097200-1100800	Genic enhancers	Primary T cells from cord blood	blood
26	chr10:1097200-1100800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr10:1097400-1100200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:1097400-1100200	Weak transcription	Fetal Heart	heart
29	chr10:1097400-1100400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr10:1097400-1100400	Strong transcription	HSMM	muscle
31	chr10:1097400-1100600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr10:1097400-1100800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:1097600-1100200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:1097600-1100200	Strong transcription	Left Ventricle	heart
35	chr10:1097600-1100200	Weak transcription	Hela-S3	cervix
36	chr10:1097600-1100400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr10:1097600-1100400	Weak transcription	Brain Substantia Nigra	brain
38	chr10:1097600-1100800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr10:1097600-1100800	Weak transcription	Brain Angular Gyrus	brain
40	chr10:1097800-1100400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:1097800-1100400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr10:1097800-1100400	Genic enhancers	Dnd41	blood
43	chr10:1097800-1100800	Weak transcription	HSMMtube	muscle
44	chr10:1098000-1100200	Strong transcription	Thymus	Thymus
45	chr10:1098000-1100400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:1098200-1100200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr10:1098200-1100200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:1098200-1100200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr10:1098200-1100200	Strong transcription	Adipose Nuclei	Adipose
50	chr10:1098200-1100200	Strong transcription	Brain Anterior Caudate	brain

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