Variant report

Variant	rs6962593
Chromosome Location	chr7:140177978-140177979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140175625..140180151-chr7:140394567..140398370,5	MCF-7	breast:
2	chr7:140155139..140157555-chr7:140177850..140179410,2	K562	blood:
3	chr7:140176812..140180644-chr7:140393947..140398398,4	K562	blood:
4	chr7:139874986..139876906-chr7:140177718..140179514,2	MCF-7	breast:
5	chr7:139873272..139877357-chr7:140175860..140178713,3	K562	blood:
6	chr7:140176812..140179399-chr7:140395126..140397171,2	K562	blood:
7	chr7:140152800..140155716-chr7:140177894..140179850,2	MCF-7	breast:
8	chr7:140177294..140179711-chr7:140373712..140375545,2	K562	blood:
9	chr7:140176559..140178160-chr7:140351087..140353237,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000006459	Chromatin interaction
ENSG00000240889	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000146966	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000260231	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10216203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs10224992	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10226064	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10229678	0.95[EUR][1000 genomes]
rs10231547	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10243155	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244642	0.82[EUR][1000 genomes]
rs10256899	0.91[EUR][1000 genomes]
rs10257079	0.93[EUR][1000 genomes]
rs10258350	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10267810	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10269611	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10270875	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs10272040	0.92[EUR][1000 genomes]
rs10272047	0.95[EUR][1000 genomes]
rs10273061	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10275127	0.93[EUR][1000 genomes]
rs10275142	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10278060	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279172	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10280145	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10952680	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11760895	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11765962	0.82[EUR][1000 genomes]
rs11766079	0.96[EUR][1000 genomes]
rs11974068	0.91[EUR][1000 genomes]
rs11978135	0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs12216619	0.93[EUR][1000 genomes]
rs13438384	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13438583	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17161542	0.88[EUR][1000 genomes]
rs17161569	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs1969394	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2272096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363824	0.93[EUR][1000 genomes]
rs2363826	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363828	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28412759	0.93[EUR][1000 genomes]
rs28439514	0.95[EUR][1000 genomes]
rs28538447	0.93[EUR][1000 genomes]
rs28553284	0.82[EUR][1000 genomes]
rs28563126	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28667371	0.82[EUR][1000 genomes]
rs28699169	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28784908	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28785875	0.93[EUR][1000 genomes]
rs28832645	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2885922	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs28880113	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35747234	0.93[EUR][1000 genomes]
rs4385389	0.93[EUR][1000 genomes]
rs4424177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4427086	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4431522	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714045	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55833852	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55961611	0.93[EUR][1000 genomes]
rs56059991	0.96[EUR][1000 genomes]
rs56769703	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58076938	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58647694	0.96[EUR][1000 genomes]
rs59356360	0.84[AFR][1000 genomes]
rs59814044	0.91[EUR][1000 genomes]
rs60137728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61577108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62490410	0.82[EUR][1000 genomes]
rs62490429	0.95[EUR][1000 genomes]
rs62490449	0.96[EUR][1000 genomes]
rs6464773	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6464779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6951446	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6962710	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6963738	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6964170	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6966049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966056	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966930	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968931	0.91[EUR][1000 genomes]
rs6973069	0.81[EUR][1000 genomes]
rs6975307	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7777404	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7779827	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7784558	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7785094	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7786776	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7787217	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7789557	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7790232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800959	0.82[EUR][1000 genomes]
rs7805365	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7808589	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7811669	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9648837	0.93[EUR][1000 genomes]
rs9692138	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][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	nsv464734	chr7:140108096-140217670	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv608500	chr7:140108096-140217670	Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Weak transcription 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	15 gene(s)	inside rSNPs	diseases
3	esv1803443	chr7:140146694-140263109	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140156800-140178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:140170800-140178200	Weak transcription	Gastric	stomach
3	chr7:140171400-140178200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:140171600-140178000	Weak transcription	Aorta	Aorta
5	chr7:140171600-140178200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:140171600-140178200	Weak transcription	Small Intestine	intestine
7	chr7:140172200-140178000	Weak transcription	Right Ventricle	heart
8	chr7:140175600-140180000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:140176400-140178000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr7:140176600-140178000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:140176600-140178000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr7:140176600-140178200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr7:140176600-140178200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:140176600-140179400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:140176600-140179600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:140176600-140179600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:140176600-140180000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:140176800-140178200	Flanking Active TSS	Liver	Liver
19	chr7:140176800-140179600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr7:140176800-140179600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:140177000-140178000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:140177000-140178200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr7:140177000-140178200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:140177000-140178200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:140177000-140179400	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr7:140177000-140179400	Active TSS	GM12878-XiMat	blood
27	chr7:140177000-140179600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr7:140177000-140179600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:140177000-140179600	Active TSS	Fetal Intestine Small	intestine
30	chr7:140177200-140178000	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr7:140177200-140178000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:140177200-140179400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr7:140177200-140180000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr7:140177400-140178000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr7:140177400-140178000	Weak transcription	Left Ventricle	heart
36	chr7:140177400-140178000	Weak transcription	Lung	lung
37	chr7:140177400-140178000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr7:140177400-140178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:140177400-140178200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr7:140177400-140178200	Flanking Active TSS	Dnd41	blood
41	chr7:140177400-140178200	Flanking Active TSS	Hela-S3	cervix
42	chr7:140177400-140179400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:140177400-140179400	Active TSS	NHLF	lung
44	chr7:140177400-140179600	Active TSS	Fetal Intestine Large	intestine
45	chr7:140177400-140179600	Active TSS	HepG2	liver
46	chr7:140177400-140179800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:140177400-140179800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:140177400-140179800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:140177400-140179800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:140177400-140179800	Active TSS	Colonic Mucosa	Colon

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