Variant report

Variant	rs10249090
Chromosome Location	chr7:38872929-38872930
allele	C/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	RCOR1	chr7:38872840-38873046	K562	blood:	n/a	n/a
2	NR2F2	chr7:38872757-38873352	MCF-7	breast:	n/a	n/a
3	GATA3	chr7:38872856-38873349	MCF-7	breast:	n/a	n/a
4	GATA3	chr7:38872856-38873384	MCF-7	breast:	n/a	n/a
5	GATA3	chr7:38872884-38873372	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
VPS41	TF binding region

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10085898	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019065	0.88[ASN][1000 genomes]
rs10229531	0.86[ASN][1000 genomes]
rs10244901	0.86[ASN][1000 genomes]
rs10245322	0.86[ASN][1000 genomes]
rs10245333	0.86[ASN][1000 genomes]
rs10250120	0.86[ASN][1000 genomes]
rs10251632	0.84[ASN][1000 genomes]
rs10254617	0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10262154	0.82[CEU][hapmap]
rs10266910	0.86[ASN][1000 genomes]
rs10268253	0.82[ASN][1000 genomes]
rs10269756	0.88[ASN][1000 genomes]
rs10272658	0.82[ASN][1000 genomes]
rs10274968	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10279181	0.86[ASN][1000 genomes]
rs10279990	0.86[ASN][1000 genomes]
rs10280140	0.86[ASN][1000 genomes]
rs10281823	0.86[ASN][1000 genomes]
rs10951576	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951578	0.86[ASN][1000 genomes]
rs1155507	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1155513	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11765467	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772408	0.86[ASN][1000 genomes]
rs11980197	0.88[ASN][1000 genomes]
rs11980627	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11983390	0.88[ASN][1000 genomes]
rs12533017	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535711	0.90[ASN][1000 genomes]
rs12672018	0.86[ASN][1000 genomes]
rs13228087	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs13237387	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1468347	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473138	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473139	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17618395	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17619021	0.86[ASN][1000 genomes]
rs17680408	0.94[ASN][1000 genomes]
rs17680879	0.86[ASN][1000 genomes]
rs2008199	0.86[ASN][1000 genomes]
rs2009277	0.88[ASN][1000 genomes]
rs2067683	0.86[ASN][1000 genomes]
rs2072248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074853	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2159018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2189853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2286080	0.91[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2392600	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2392601	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392603	0.86[ASN][1000 genomes]
rs2392604	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2392605	0.88[ASN][1000 genomes]
rs2392606	0.84[ASN][1000 genomes]
rs2392607	0.90[ASN][1000 genomes]
rs28369620	0.88[ASN][1000 genomes]
rs28460817	0.90[ASN][1000 genomes]
rs28680843	0.81[AFR][1000 genomes]
rs34276565	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35548426	0.92[EUR][1000 genomes]
rs3735346	0.86[ASN][1000 genomes]
rs3779122	0.96[ASN][1000 genomes]
rs3779124	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779125	0.94[ASN][1000 genomes]
rs3801111	0.86[ASN][1000 genomes]
rs3801113	0.86[ASN][1000 genomes]
rs3801114	0.86[ASN][1000 genomes]
rs3801115	0.86[ASN][1000 genomes]
rs3801116	0.86[ASN][1000 genomes]
rs3801119	0.86[ASN][1000 genomes]
rs3801124	0.86[ASN][1000 genomes]
rs3801126	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs3801127	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs3801128	0.96[ASN][1000 genomes]
rs3801132	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236355	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4610638	0.98[EUR][1000 genomes]
rs4623319	0.86[ASN][1000 genomes]
rs4720303	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs4720306	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4723789	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4723791	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4723792	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723798	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4723800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56980069	0.86[ASN][1000 genomes]
rs59626436	0.86[ASN][1000 genomes]
rs59995998	0.86[ASN][1000 genomes]
rs62443565	0.86[ASN][1000 genomes]
rs62443566	0.86[ASN][1000 genomes]
rs62443573	0.86[ASN][1000 genomes]
rs62444126	0.92[ASN][1000 genomes]
rs62444137	0.96[ASN][1000 genomes]
rs62444140	0.96[ASN][1000 genomes]
rs6415270	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6462864	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6462865	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs6462868	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462870	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943746	0.86[ASN][1000 genomes]
rs6945239	0.88[ASN][1000 genomes]
rs6946636	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6948026	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6955677	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6957565	0.95[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6959858	0.96[ASN][1000 genomes]
rs6960585	0.86[ASN][1000 genomes]
rs6963364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966738	0.86[ASN][1000 genomes]
rs6968196	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973415	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6974795	0.88[ASN][1000 genomes]
rs6979578	0.91[EUR][1000 genomes]
rs73121396	0.81[AFR][1000 genomes]
rs73123612	0.96[ASN][1000 genomes]
rs73127433	0.86[ASN][1000 genomes]
rs7776996	0.88[ASN][1000 genomes]
rs7777039	0.82[ASN][1000 genomes]
rs7782927	0.86[ASN][1000 genomes]
rs7788383	0.86[ASN][1000 genomes]
rs7793692	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7798033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7811383	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8180877	0.88[ASN][1000 genomes]
rs917320	0.86[ASN][1000 genomes]
rs917321	0.86[ASN][1000 genomes]
rs917322	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs929422	1.00[ASN][1000 genomes]
rs9639805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9655397	0.96[ASN][1000 genomes]
rs976353	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs982392	1.00[CHB][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38863000-38876800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
9	chr7:38863800-38879600	Weak transcription	Fetal Lung	lung
10	chr7:38864000-38874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:38865600-38873000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:38865800-38879600	Weak transcription	Right Atrium	heart
13	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:38866400-38876800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:38866400-38877000	Weak transcription	Primary T cells from cord blood	blood
16	chr7:38866800-38877000	Weak transcription	Primary B cells from cord blood	blood
17	chr7:38867200-38876800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:38867400-38873000	Weak transcription	Gastric	stomach
19	chr7:38867400-38877800	Weak transcription	Fetal Brain Male	brain
20	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
21	chr7:38867600-38879600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:38868800-38873800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:38870000-38876600	Weak transcription	GM12878-XiMat	blood
25	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:38871000-38884400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr7:38871400-38873600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:38871400-38880400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
32	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:38871600-38873800	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:38871600-38875400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr7:38871600-38878400	Weak transcription	Brain Angular Gyrus	brain
36	chr7:38871600-38879800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:38872400-38873200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:38872800-38873000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr7:38872800-38873200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:38872800-38873200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:38872800-38873200	Enhancers	Adipose Nuclei	Adipose
43	chr7:38872800-38873200	Enhancers	Fetal Heart	heart
44	chr7:38872800-38873200	Enhancers	Ovary	ovary
45	chr7:38872800-38873200	Enhancers	Pancreas	Pancrea

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