Variant report

Variant	rs38734
Chromosome Location	chr7:140706708-140706709
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140706694-140706801	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:140706615-140706735	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:140706489-140706711	K562	blood:	n/a	n/a
4	POLR2A	chr7:140706566-140706801	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:140701510..140704472-chr7:140705422..140707944,2	MCF-7	breast:
2	chr7:140700885..140703018-chr7:140705505..140708464,2	MCF-7	breast:
3	chr7:140706633..140708979-chr7:140709208..140712077,3	MCF-7	breast:
4	chr7:140705945..140708045-chr7:140709551..140711104,2	K562	blood:
5	chr7:140705059..140707957-chr7:140712548..140716287,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273081	TF binding region
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10215245	0.91[ASN][1000 genomes]
rs10240888	0.83[EUR][1000 genomes]
rs1044927	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10488098	0.89[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1089264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10952364	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs12538296	0.82[ASN][1000 genomes]
rs12703284	0.82[ASN][1000 genomes]
rs13234490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs13236704	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs13438609	0.80[EUR][1000 genomes]
rs1476816	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1533933	0.91[ASN][1000 genomes]
rs17622717	0.89[CEU][hapmap]
rs17695341	0.89[CEU][hapmap]
rs17695623	0.89[CEU][hapmap]
rs17695707	0.89[CEU][hapmap]
rs17695935	0.89[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs17695995	0.89[CEU][hapmap]
rs1860720	0.91[ASN][1000 genomes]
rs1961288	0.82[ASN][1000 genomes]
rs2079827	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2079978	0.91[ASN][1000 genomes]
rs246739	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688430	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805116	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs38715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38717	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38718	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38719	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs38720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38726	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38731	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38736	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4726225	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs488795	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs490810	0.82[ASN][1000 genomes]
rs512177	0.82[ASN][1000 genomes]
rs512509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs528957	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs533441	0.82[ASN][1000 genomes]
rs544081	0.84[ASN][1000 genomes]
rs545121	0.82[ASN][1000 genomes]
rs557962	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs569584	0.84[ASN][1000 genomes]
rs579518	0.82[ASN][1000 genomes]
rs58901822	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62485391	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62485451	0.83[EUR][1000 genomes]
rs62485452	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62485453	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6464217	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6464260	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs6464284	0.82[ASN][1000 genomes]
rs6662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6967214	0.89[ASN][1000 genomes]
rs6971577	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7792447	0.91[ASN][1000 genomes]
rs7801518	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7810757	0.89[CEU][hapmap]
rs801117	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs801155	0.84[ASN][1000 genomes]
rs801159	0.82[ASN][1000 genomes]
rs9274	1.00[CHB][hapmap]

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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140698600-140713000	Weak transcription	Psoas Muscle	Psoas
2	chr7:140699600-140713800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140701400-140713400	Weak transcription	NHLF	lung
4	chr7:140702000-140707400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:140702000-140709200	Weak transcription	Fetal Kidney	kidney
6	chr7:140702800-140713200	Weak transcription	HSMMtube	muscle
7	chr7:140703200-140709400	Weak transcription	HSMM	muscle
8	chr7:140703200-140713800	Weak transcription	Stomach Mucosa	stomach
9	chr7:140703400-140713800	Weak transcription	Gastric	stomach
10	chr7:140703600-140710800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:140703600-140713800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:140703600-140713800	Weak transcription	Lung	lung
13	chr7:140703800-140707200	Weak transcription	Spleen	Spleen
14	chr7:140703800-140707400	Weak transcription	Fetal Intestine Small	intestine
15	chr7:140703800-140707600	Weak transcription	HepG2	liver
16	chr7:140703800-140709200	Weak transcription	Osteobl	bone
17	chr7:140704000-140713800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:140704200-140707000	Weak transcription	Ovary	ovary
19	chr7:140704200-140708200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:140704400-140707200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:140704400-140711400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:140704800-140707800	Strong transcription	Primary T cells from cord blood	blood
23	chr7:140704800-140710400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:140704800-140710400	Strong transcription	Fetal Brain Female	brain
25	chr7:140704800-140710600	Strong transcription	Fetal Muscle Leg	muscle
26	chr7:140704800-140711000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:140705000-140709800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr7:140705000-140710200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:140705000-140710200	Strong transcription	Fetal Intestine Large	intestine
30	chr7:140705000-140710800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr7:140705000-140711000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:140705000-140712200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:140705000-140713600	Weak transcription	NH-A	brain
34	chr7:140705200-140707000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:140705200-140707600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:140705200-140707600	Strong transcription	Aorta	Aorta
37	chr7:140705200-140707800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:140705200-140708400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr7:140705200-140708400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:140705200-140710000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr7:140705200-140710000	Strong transcription	Brain Hippocampus Middle	brain
42	chr7:140705200-140710000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr7:140705200-140710200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:140705200-140710400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:140705200-140710400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:140705200-140710800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr7:140705200-140710800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:140705200-140710800	Strong transcription	Liver	Liver
49	chr7:140705200-140710800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:140705200-140710800	Strong transcription	Fetal Muscle Trunk	muscle

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