Variant report

Variant	rs6580770
Chromosome Location	chr12:51195748-51195749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51194188..51196779-chr12:51231539..51234008,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10506296	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10735827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10747590	0.88[ASN][1000 genomes]
rs10747592	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10747593	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10783388	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10783390	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs10876082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876085	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876088	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876091	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11169553	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169556	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12320201	0.81[EUR][1000 genomes]
rs1402693	1.00[CEU][hapmap]
rs1521515	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1521517	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs1561422	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs17124888	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17124907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1815010	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246840	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2252595	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs2684886	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2684890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2684891	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2684902	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2684906	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs2700486	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2947617	0.81[EUR][1000 genomes]
rs3803181	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4143663	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768862	0.92[ASN][1000 genomes]
rs4768909	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768915	0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4768920	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56818625	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57328764	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58301497	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59284993	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61926300	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6580766	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132443	0.86[EUR][1000 genomes]
rs7135222	0.81[EUR][1000 genomes]
rs7301125	0.81[EUR][1000 genomes]
rs7303202	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7304793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308872	0.84[ASN][1000 genomes]
rs7487150	0.94[ASN][1000 genomes]
rs7959129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7964642	0.95[ASN][1000 genomes]
rs7969251	0.81[ASN][1000 genomes]
rs7979474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829133	0.83[JPT][hapmap]
rs865490	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939631	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs951591	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs9634264	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51189600-51195800	ZNF genes & repeats	GM12878-XiMat	blood
4	chr12:51189600-51196400	Strong transcription	HSMM	muscle
5	chr12:51189600-51199800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:51190200-51204000	Weak transcription	Gastric	stomach
7	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
8	chr12:51190600-51196400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:51190600-51197400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:51191400-51196600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr12:51192400-51195800	ZNF genes & repeats	A549	lung
12	chr12:51192400-51195800	ZNF genes & repeats	Dnd41	blood
13	chr12:51193200-51196400	Strong transcription	Placenta	Placenta
14	chr12:51193200-51200000	Weak transcription	Thymus	Thymus
15	chr12:51193200-51200000	Weak transcription	Spleen	Spleen
16	chr12:51193200-51203200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:51193200-51204400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:51193200-51207600	Weak transcription	Fetal Heart	heart
19	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
22	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
23	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
24	chr12:51193400-51203200	Weak transcription	Colonic Mucosa	Colon
25	chr12:51193400-51204000	Weak transcription	Psoas Muscle	Psoas
26	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:51193600-51195800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:51193600-51195800	Strong transcription	Hela-S3	cervix
29	chr12:51193800-51202800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:51193800-51204200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:51193800-51204400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:51193800-51204400	Weak transcription	Fetal Brain Male	brain
33	chr12:51194000-51195800	Strong transcription	HepG2	liver
34	chr12:51194000-51200000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:51194000-51200000	Weak transcription	K562	blood
36	chr12:51194000-51203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:51194000-51203400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:51194000-51203400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:51194000-51204200	Weak transcription	NHLF	lung
40	chr12:51194000-51204400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:51194000-51204400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:51194000-51204400	Weak transcription	NHEK	skin
43	chr12:51194000-51204600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:51194200-51196200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:51194200-51196600	Strong transcription	Primary T cells from cord blood	blood
46	chr12:51194200-51203200	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:51194200-51203200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:51194200-51203400	Weak transcription	Brain Substantia Nigra	brain
49	chr12:51194400-51196400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:51194400-51200000	Weak transcription	Adipose Nuclei	Adipose

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