Variant report

Variant	rs10877883
Chromosome Location	chr12:62980580-62980581
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62977946..62980694-chr12:63003640..63006233,2	MCF-7	breast:
2	chr12:62978537..62982109-chr12:62993246..62999032,10	MCF-7	breast:
3	chr12:62979289..62980893-chr12:62991246..62992816,2	K562	blood:
4	chr12:62975073..62982220-chr12:62994233..63000379,9	K562	blood:
5	chr12:62978077..62985603-chr12:62994484..62999339,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257354	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000199179	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10128830	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10128959	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10161549	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10219555	0.84[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10219765	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735907	0.84[EUR][1000 genomes]
rs10735909	0.83[EUR][1000 genomes]
rs10747966	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10784299	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784302	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784303	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784306	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784307	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877860	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877863	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877865	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877866	0.85[CEU][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877868	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877869	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877872	0.81[ASN][1000 genomes]
rs10877873	0.88[CEU][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877876	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877878	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877880	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877882	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877885	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877886	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877887	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877888	0.81[CEU][hapmap];0.84[ASN][1000 genomes]
rs11174493	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11174497	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11174507	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11174513	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11174520	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11174534	0.84[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174538	0.83[ASN][1000 genomes]
rs11174539	0.86[EUR][1000 genomes]
rs11174540	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174541	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174542	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174545	0.84[ASN][1000 genomes]
rs11174550	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174559	0.81[ASN][1000 genomes]
rs12227568	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12300696	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12305077	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12309683	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12357	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578200	0.85[EUR][1000 genomes]
rs12580048	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12581171	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12809279	0.80[AMR][1000 genomes]
rs12810119	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12829103	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498713	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029937	0.84[EUR][1000 genomes]
rs2047478	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047479	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2220980	0.85[EUR][1000 genomes]
rs35409044	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763021	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs4763174	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4763177	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763179	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763180	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581452	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581454	0.84[ASN][1000 genomes]
rs7134302	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7136993	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71453871	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7294404	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7298782	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302027	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7316612	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957417	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7963657	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975183	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7975560	0.84[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
3	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
5	chr12:62944600-62989000	Weak transcription	Colonic Mucosa	Colon
6	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:62950600-62982600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:62950600-62991200	Weak transcription	Gastric	stomach
9	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
10	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
11	chr12:62950800-62995000	Weak transcription	NHEK	skin
12	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:62951200-62986800	Weak transcription	Brain Angular Gyrus	brain
15	chr12:62951200-62988600	Weak transcription	Spleen	Spleen
16	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
17	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
18	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:62954800-62989000	Weak transcription	Lung	lung
21	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
22	chr12:62955000-62987800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:62955200-62995200	Weak transcription	HepG2	liver
24	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
26	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:62959600-62995600	Weak transcription	NHLF	lung
28	chr12:62960000-62982800	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:62961200-62995600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:62961400-62982600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:62961400-62989200	Weak transcription	Psoas Muscle	Psoas
32	chr12:62961400-62995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:62961400-62995600	Weak transcription	Brain Germinal Matrix	brain
34	chr12:62961600-62995600	Weak transcription	Fetal Brain Female	brain
35	chr12:62961800-62995600	Weak transcription	Brain Substantia Nigra	brain
36	chr12:62962000-62995600	Weak transcription	HMEC	breast
37	chr12:62962400-62982000	Weak transcription	HUVEC	blood vessel
38	chr12:62963200-62995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:62964000-62995800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:62965400-62992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:62965600-62982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:62965800-62982400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:62966000-62980600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:62966200-62982400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:62966200-62995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:62966200-62995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:62966400-62985200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:62966400-62995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:62966400-62995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:62966600-62983800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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