Variant report

Variant	rs7078478
Chromosome Location	chr10:96325677-96325678
allele	A/G
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	chr10:96325669-96325836	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr10:96325665-96325937	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:96325514-96326061	GM12892	blood:	n/a	n/a
4	POLR2A	chr10:96325327-96326084	GM12892	blood:	n/a	n/a
5	POLR2A	chr10:96325675-96325798	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
HELLS	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10786168	0.83[JPT][hapmap]
rs10786169	1.00[JPT][hapmap]
rs10882460	0.83[JPT][hapmap]
rs10882463	0.83[JPT][hapmap]
rs10882474	0.83[JPT][hapmap]
rs10882475	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882477	0.83[JPT][hapmap]
rs11187939	0.81[JPT][hapmap]
rs11187940	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs11187944	0.82[JPT][hapmap]
rs11187952	0.83[JPT][hapmap]
rs11187960	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs11187972	0.90[JPT][hapmap]
rs11187998	0.80[JPT][hapmap]
rs11188009	0.83[JPT][hapmap]
rs11188012	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11188019	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11188020	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11188036	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11188040	0.80[JPT][hapmap]
rs11638	1.00[JPT][hapmap]
rs12218213	0.80[JPT][hapmap]
rs12218216	0.80[JPT][hapmap]
rs12219906	0.80[JPT][hapmap]
rs12221475	0.82[JPT][hapmap]
rs12573638	0.80[JPT][hapmap]
rs1334595	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1359263	0.80[JPT][hapmap]
rs1409655	0.83[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs1749356	0.80[JPT][hapmap]
rs1931757	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1969815	0.80[JPT][hapmap]
rs1977288	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977291	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1980741	1.00[JPT][hapmap]
rs2031323	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2148553	0.80[JPT][hapmap]
rs2274417	0.80[JPT][hapmap]
rs2281791	0.83[JPT][hapmap]
rs2860821	0.80[JPT][hapmap]
rs2860840	0.83[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs3740358	0.83[JPT][hapmap]
rs3781262	0.82[JPT][hapmap]
rs4351744	1.00[JPT][hapmap]
rs4564258	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4600139	0.84[AMR][1000 genomes]
rs480032	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs4918402	0.83[JPT][hapmap]
rs4918409	0.80[JPT][hapmap]
rs4918417	0.84[JPT][hapmap]
rs4918419	0.80[JPT][hapmap]
rs517784	0.83[JPT][hapmap]
rs556055	0.83[JPT][hapmap]
rs6583941	0.82[EUR][1000 genomes]
rs6583942	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs6583947	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs692872	0.83[JPT][hapmap]
rs701885	0.83[JPT][hapmap]
rs7075182	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7078811	1.00[JPT][hapmap]
rs7083898	1.00[JPT][hapmap]
rs7087798	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7088008	0.82[EUR][1000 genomes]
rs7092129	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7096007	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7900007	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7906843	1.00[JPT][hapmap]
rs7906968	0.80[JPT][hapmap]
rs7913343	0.93[JPT][hapmap]
rs7921721	1.00[JPT][hapmap]
rs7922956	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs912466	0.80[JPT][hapmap]
rs955694	0.80[JPT][hapmap]
rs9645542	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306400-96330600	Weak transcription	Placenta	Placenta
2	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
4	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:96306400-96371000	Weak transcription	Ovary	ovary
7	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:96306800-96330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
14	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
17	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:96307000-96375000	Weak transcription	Osteobl	bone
19	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
20	chr10:96307600-96327800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:96307600-96356000	Weak transcription	NHDF-Ad	bronchial
22	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
23	chr10:96307800-96348200	Weak transcription	NHEK	skin
24	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:96309400-96340800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:96309400-96354000	Weak transcription	K562	blood
28	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:96310200-96339800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr10:96310400-96339800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:96312200-96334400	Strong transcription	A549	lung
33	chr10:96312200-96354000	Weak transcription	Gastric	stomach
34	chr10:96312800-96372200	Strong transcription	Dnd41	blood
35	chr10:96314000-96330800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:96314200-96339800	Strong transcription	Fetal Thymus	thymus
37	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:96314400-96325800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:96315000-96369200	Weak transcription	Fetal Kidney	kidney
40	chr10:96315200-96332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr10:96315600-96343800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr10:96315600-96345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr10:96316000-96330200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:96316000-96338200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:96316000-96371400	Weak transcription	Fetal Brain Female	brain
46	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:96316200-96357600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr10:96317000-96332600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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