Variant report

Variant	rs2255074
Chromosome Location	chr12:57030026-57030027
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:26)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57026160..57032326-chr12:57079667..57084551,17	K562	blood:
2	chr12:56726222..56728684-chr12:57029167..57031416,2	K562	blood:
3	chr12:56519055..56522038-chr12:57029162..57030731,2	K562	blood:
4	chr12:56861952..56864525-chr12:57027360..57030112,3	MCF-7	breast:
5	chr12:57003620..57005950-chr12:57028617..57030192,2	MCF-7	breast:
6	chr12:57029847..57032338-chr12:57145228..57146729,2	MCF-7	breast:
7	chr12:56708298..56710997-chr12:57029134..57031889,3	MCF-7	breast:
8	chr12:57027161..57032164-chr12:57080546..57084524,13	MCF-7	breast:
9	chr12:57029606..57030383-chr6:12008234..12009003,2	Hela-S3	cervix:
10	chr12:56992973..56997884-chr12:57027374..57031905,8	K562	blood:
11	chr12:57026457..57031197-chr12:57479410..57483153,5	MCF-7	breast:
12	chr12:57027023..57035553-chr12:57079936..57085201,18	MCF-7	breast:
13	chr12:57028651..57034442-chr12:57080412..57084452,17	K562	blood:
14	chr12:56551730..56554656-chr12:57027945..57032236,3	K562	blood:
15	chr12:57028665..57030374-chr12:57480509..57482064,2	K562	blood:
16	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:
17	chr12:56753830..56756625-chr12:57028420..57030715,2	MCF-7	breast:
18	chr12:57029325..57031901-chr12:57117186..57120147,2	K562	blood:
19	chr12:57028905..57032364-chr12:57143305..57146712,4	K562	blood:
20	chr12:56997043..57002825-chr12:57025405..57031317,7	MCF-7	breast:
21	chr12:57026523..57033046-chr12:57115223..57120839,17	MCF-7	breast:
22	chr12:56993930..56997262-chr12:57028560..57031023,3	K562	blood:
23	chr12:57028511..57031502-chr12:57144814..57146323,2	MCF-7	breast:
24	chr12:57028481..57030405-chr12:57144099..57146089,2	K562	blood:
25	chr12:57029241..57032243-chr12:57118930..57120997,3	MCF-7	breast:
26	chr12:57007109..57010688-chr12:57028709..57032558,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP5B-1	chr12:57029966-57030077	NONHSAT028835

No data

Variant related genes	Relation type
ENSG00000095951	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000175336	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1020848	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1026565	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10747769	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10876913	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876914	0.99[ASN][1000 genomes]
rs10876915	0.99[ASN][1000 genomes]
rs10876916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1107479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171914	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171916	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171917	0.99[ASN][1000 genomes]
rs11171951	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs11835120	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837319	0.99[ASN][1000 genomes]
rs12229457	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465081	0.99[ASN][1000 genomes]
rs1466382	0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs1563896	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563897	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962963	0.87[ASN][1000 genomes]
rs1979325	0.93[CHB][hapmap]
rs2035081	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs2242497	0.85[YRI][hapmap]
rs2290893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290894	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs2926740	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926741	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs2926743	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2950387	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2950388	0.99[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2950393	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2950394	0.99[ASN][1000 genomes]
rs2958123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2958124	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958127	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs2958130	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs2958145	0.99[ASN][1000 genomes]
rs2958146	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2958148	0.94[CEU][hapmap]
rs2958149	0.87[CHB][hapmap]
rs2958153	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2958154	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2958155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3214051	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs36012661	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759028	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4759254	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs67046307	0.99[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap]
rs7297289	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303216	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313074	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7315472	0.99[ASN][1000 genomes]
rs73337030	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957300	0.82[EUR][1000 genomes]
rs7967600	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs7972420	0.94[ASN][1000 genomes]
rs7973157	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975783	0.93[ASN][1000 genomes]
rs7978685	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7980317	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap]
rs7980378	0.93[ASN][1000 genomes]
rs7980835	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs898609	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs898611	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs9368	0.81[CHB][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap]
rs941207	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634246	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9634247	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634277	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9989034	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2255074	RAB5B	cis	cerebellum	SCAN
rs2255074	HOXC6	cis	cerebellum	SCAN
rs2255074	OR10A7	cis	parietal	SCAN
rs2255074	HSD17B6	cis	cerebellum	SCAN
rs2255074	IL23A	cis	cerebellum	SCAN
rs2255074	PRIM1	cis	cerebellum	SCAN
rs2255074	PRIM1	cis	parietal	SCAN
rs2255074	STAT6	cis	parietal	SCAN
rs2255074	CELA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57025400-57030600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:57025400-57031400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:57026400-57030600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:57026400-57030800	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr12:57026600-57031200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:57027200-57031200	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:57027600-57030200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:57027600-57030400	Active TSS	NHDF-Ad	bronchial
9	chr12:57027600-57030600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:57027600-57030800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:57027600-57030800	Active TSS	Thymus	Thymus
12	chr12:57027600-57031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr12:57027800-57030200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:57027800-57030200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:57027800-57030200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:57027800-57030400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:57027800-57030400	Active TSS	Ovary	ovary
18	chr12:57027800-57030600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:57027800-57030600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:57027800-57030600	Active TSS	Esophagus	oesophagus
21	chr12:57027800-57030600	Active TSS	Gastric	stomach
22	chr12:57027800-57030600	Active TSS	Placenta Amnion	Placenta Amnion
23	chr12:57027800-57030800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr12:57027800-57030800	Flanking Active TSS	Dnd41	blood
25	chr12:57028000-57030200	Active TSS	Lung	lung
26	chr12:57028000-57030200	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr12:57028000-57030400	Active TSS	NHLF	lung
28	chr12:57028000-57030600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:57028000-57030600	Active TSS	Aorta	Aorta
30	chr12:57028200-57030200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:57028200-57030200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:57028200-57030400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr12:57028200-57030400	Active TSS	Small Intestine	intestine
34	chr12:57028200-57030600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr12:57028200-57030600	Active TSS	Left Ventricle	heart
36	chr12:57028200-57030600	Active TSS	Psoas Muscle	Psoas
37	chr12:57028200-57031000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:57028400-57030400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:57028400-57030600	Active TSS	Colon Smooth Muscle	Colon
40	chr12:57028400-57031000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:57028800-57030600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:57029000-57030200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:57029000-57030400	Bivalent/Poised TSS	HepG2	liver
44	chr12:57029000-57030600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:57029000-57030600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:57029000-57030600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:57029000-57030600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:57029000-57030600	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr12:57029000-57030600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr12:57029000-57030600	Flanking Active TSS	Fetal Brain Female	brain

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