Variant report

Variant	rs10409
Chromosome Location	chr10:43881921-43881922
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43849658..43851212-chr10:43881372..43882946,2	MCF-7	breast:
2	chr10:43868177..43875753-chr10:43880229..43888906,15	MCF-7	breast:
3	chr10:43879008..43883052-chr10:43949060..43952010,4	K562	blood:

Variant related genes	Relation type
ENSG00000150201	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10466239	0.86[ASN][1000 genomes]
rs10899791	0.92[ASN][1000 genomes]
rs10899793	0.92[ASN][1000 genomes]
rs10899794	0.89[JPT][hapmap]
rs10899796	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899797	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10899800	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899801	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899802	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899803	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];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899806	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899808	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238525	0.90[ASN][1000 genomes]
rs11238530	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238532	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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238553	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];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238558	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238566	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11238572	0.80[AMR][1000 genomes]
rs11525297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11814409	0.85[CHB][hapmap];0.84[YRI][hapmap]
rs11815101	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12217904	0.82[YRI][hapmap]
rs12220230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12220528	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245541	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12250140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12254798	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12261855	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262836	0.80[AMR][1000 genomes]
rs13376803	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376924	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17153534	0.92[ASN][1000 genomes]
rs17153701	0.86[ASW][hapmap]
rs2247979	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2247981	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2250444	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2252783	0.80[JPT][hapmap]
rs2261636	0.90[JPT][hapmap]
rs28865415	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4648316	0.92[ASN][1000 genomes]
rs4948726	0.90[JPT][hapmap]
rs56198445	0.86[ASN][1000 genomes]
rs59383062	0.92[ASN][1000 genomes]
rs6593513	0.80[JPT][hapmap]
rs7099802	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905676	0.90[JPT][hapmap]
rs7907179	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921001	0.90[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:127 , 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	chr10:43870000-43882000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:43870200-43882000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:43870200-43882000	Weak transcription	Brain Substantia Nigra	brain
6	chr10:43870400-43882000	Weak transcription	Brain Angular Gyrus	brain
7	chr10:43873200-43890200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:43873400-43882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:43873400-43891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr10:43873800-43882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:43873800-43882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:43874400-43882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:43877200-43882000	Weak transcription	Psoas Muscle	Psoas
14	chr10:43877400-43882000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:43878600-43882600	Weak transcription	Fetal Brain Male	brain
16	chr10:43878800-43882200	Weak transcription	Fetal Kidney	kidney
17	chr10:43879000-43882000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:43879200-43882000	Weak transcription	Aorta	Aorta
19	chr10:43879200-43882000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:43879200-43889800	Strong transcription	Brain Germinal Matrix	brain
21	chr10:43879400-43882000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:43879400-43882000	Weak transcription	Fetal Intestine Small	intestine
23	chr10:43879400-43882000	Weak transcription	Ovary	ovary
24	chr10:43879400-43889400	Strong transcription	Fetal Brain Female	brain
25	chr10:43879600-43882000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:43879600-43882600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr10:43879600-43885800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:43879600-43889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:43879800-43883000	Strong transcription	Primary B cells from cord blood	blood
30	chr10:43879800-43883000	Strong transcription	Primary T cells from cord blood	blood
31	chr10:43879800-43889400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr10:43879800-43890600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr10:43880000-43882000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr10:43880000-43882000	Strong transcription	Fetal Thymus	thymus
35	chr10:43880000-43882200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr10:43880000-43883200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:43880000-43885400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:43880000-43885400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:43880000-43886200	Strong transcription	Adipose Nuclei	Adipose
40	chr10:43880000-43888200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:43880000-43889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:43880000-43889600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:43880000-43889600	Strong transcription	Thymus	Thymus
44	chr10:43880000-43890200	Strong transcription	Fetal Muscle Leg	muscle
45	chr10:43880000-43890200	Strong transcription	HSMMtube	muscle
46	chr10:43880000-43890400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr10:43880000-43890800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr10:43880200-43882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:43880200-43882000	Weak transcription	Right Ventricle	heart
50	chr10:43880200-43882000	Weak transcription	Small Intestine	intestine

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