Variant report

Variant	rs7920539
Chromosome Location	chr10:43880833-43880834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43855647..43857752-chr10:43878006..43881075,3	MCF-7	breast:
2	chr10:43868177..43875753-chr10:43880229..43888906,15	MCF-7	breast:
3	chr10:43858007..43859575-chr10:43879795..43881644,2	MCF-7	breast:
4	chr10:43879008..43883052-chr10:43949060..43952010,4	K562	blood:
5	chr10:43879370..43881344-chr10:43930901..43933311,2	MCF-7	breast:
6	chr10:43858972..43861250-chr10:43879046..43881690,2	K562	blood:

Variant related genes	Relation type
ENSG00000243660	Chromatin interaction
ENSG00000150201	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10732897	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10793430	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10899794	0.85[JPT][hapmap]
rs10899797	0.85[JPT][hapmap]
rs10899798	0.99[ASN][1000 genomes]
rs10899799	0.99[ASN][1000 genomes]
rs11238542	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1126487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126709	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1416226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2066043	0.96[ASN][1000 genomes]
rs2066044	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2247860	0.94[ASN][1000 genomes]
rs2247979	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2247981	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2248332	0.89[ASN][1000 genomes]
rs2248335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2248469	0.94[ASN][1000 genomes]
rs2248706	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250444	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2252783	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2252785	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2252804	0.86[ASN][1000 genomes]
rs2256495	0.96[ASN][1000 genomes]
rs2256613	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259045	0.96[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];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2260162	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2260200	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2261636	0.85[JPT][hapmap]
rs2261665	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265886	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2265954	0.91[ASN][1000 genomes]
rs2393954	0.84[ASN][1000 genomes]
rs2492403	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2492405	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2492408	0.93[ASN][1000 genomes]
rs2492409	0.94[ASN][1000 genomes]
rs2492410	0.94[ASN][1000 genomes]
rs2492411	0.94[ASN][1000 genomes]
rs2492412	0.91[ASN][1000 genomes]
rs2493648	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2812797	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2819021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2819026	0.91[ASN][1000 genomes]
rs2999276	0.99[ASN][1000 genomes]
rs2999282	0.96[ASN][1000 genomes]
rs2999287	0.86[ASN][1000 genomes]
rs3000708	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3006408	0.83[ASN][1000 genomes]
rs3750890	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4367906	0.83[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4551711	0.91[ASN][1000 genomes]
rs4559639	0.90[ASN][1000 genomes]
rs4584528	0.91[ASN][1000 genomes]
rs4597022	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4948726	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs56407131	0.82[EUR][1000 genomes]
rs6421744	0.83[ASN][1000 genomes]
rs6593513	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs7069214	0.91[ASN][1000 genomes]
rs7070769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081729	0.86[ASN][1000 genomes]
rs7089290	0.82[ASN][1000 genomes]
rs7092599	0.99[ASN][1000 genomes]
rs7894374	0.99[ASN][1000 genomes]
rs7905676	0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7914140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7918726	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9422371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
3	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43858600-43891000	Weak transcription	Right Atrium	heart
2	chr10:43869200-43882000	Weak transcription	Left Ventricle	heart
3	chr10:43870000-43881200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:43870000-43882000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:43870200-43881000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:43870200-43882000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:43870200-43882000	Weak transcription	Brain Substantia Nigra	brain
8	chr10:43870400-43881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:43870400-43881600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:43870400-43882000	Weak transcription	Brain Angular Gyrus	brain
11	chr10:43871200-43881600	Weak transcription	Brain Hippocampus Middle	brain
12	chr10:43872600-43881000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:43873200-43881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:43873200-43890200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:43873400-43881000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:43873400-43881000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:43873400-43881000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:43873400-43881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:43873400-43881400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr10:43873400-43881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr10:43873400-43882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:43873400-43891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr10:43873800-43881000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr10:43873800-43881000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr10:43873800-43882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:43873800-43882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:43874400-43882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:43876000-43881800	Weak transcription	Colon Smooth Muscle	Colon
29	chr10:43877200-43882000	Weak transcription	Psoas Muscle	Psoas
30	chr10:43877400-43882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:43877600-43881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr10:43878000-43881600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr10:43878400-43881600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr10:43878600-43882600	Weak transcription	Fetal Brain Male	brain
35	chr10:43878800-43882200	Weak transcription	Fetal Kidney	kidney
36	chr10:43879000-43882000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr10:43879200-43881000	Weak transcription	HUVEC	blood vessel
38	chr10:43879200-43881600	Weak transcription	Fetal Lung	lung
39	chr10:43879200-43881600	Weak transcription	NHDF-Ad	bronchial
40	chr10:43879200-43882000	Weak transcription	Aorta	Aorta
41	chr10:43879200-43882000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:43879200-43889800	Strong transcription	Brain Germinal Matrix	brain
43	chr10:43879400-43881800	Weak transcription	K562	blood
44	chr10:43879400-43882000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:43879400-43882000	Weak transcription	Fetal Intestine Small	intestine
46	chr10:43879400-43882000	Weak transcription	Ovary	ovary
47	chr10:43879400-43889400	Strong transcription	Fetal Brain Female	brain
48	chr10:43879600-43881200	Enhancers	Fetal Heart	heart
49	chr10:43879600-43881200	Weak transcription	HepG2	liver
50	chr10:43879600-43882000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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