Variant report

Variant	rs6547636
Chromosome Location	chr2:86100563-86100564
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86098331..86101203-chr2:86132798..86134488,2	K562	blood:
2	chr2:86098928..86100914-chr2:86276090..86278051,2	MCF-7	breast:
3	chr2:86067734..86070701-chr2:86099975..86102346,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10204648	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10496320	0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10865480	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127003	0.96[ASN][1000 genomes]
rs11127004	0.96[ASN][1000 genomes]
rs11127006	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11127007	0.95[ASN][1000 genomes]
rs11127008	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11127009	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478916	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12614498	0.88[CHB][hapmap];0.96[ASN][1000 genomes]
rs12618873	0.96[ASN][1000 genomes]
rs12622987	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13014421	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13014890	0.83[ASN][1000 genomes]
rs13016226	0.95[ASN][1000 genomes]
rs1543972	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17026675	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17026750	0.82[CEU][hapmap]
rs1878898	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap]
rs1878904	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap]
rs1878905	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280312	0.86[ASN][1000 genomes]
rs2577768	0.88[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2577769	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2679710	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2679711	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2679712	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap]
rs2679713	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2679722	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs3770097	0.86[ASN][1000 genomes]
rs3810821	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4832016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832217	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap]
rs56049132	0.96[ASN][1000 genomes]
rs56083339	0.96[ASN][1000 genomes]
rs62147537	0.94[ASN][1000 genomes]
rs62147538	0.96[ASN][1000 genomes]
rs62147540	0.96[ASN][1000 genomes]
rs6547638	0.81[ASW][hapmap]
rs6547640	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6720161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735629	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6750686	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751743	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72842060	0.80[ASN][1000 genomes]
rs7558479	0.96[ASN][1000 genomes]
rs7572209	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7587003	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764471	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs954176	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs959313	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6547636	IMMT	cis	cerebellum	SCAN
rs6547636	ST3GAL5	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86066000-86106200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:86075400-86114000	Weak transcription	Aorta	Aorta
3	chr2:86079600-86106200	Weak transcription	Brain Germinal Matrix	brain
4	chr2:86081000-86112400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:86081600-86100600	Weak transcription	NHDF-Ad	bronchial
6	chr2:86086800-86113000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:86087400-86101800	Weak transcription	Fetal Brain Female	brain
8	chr2:86088400-86105400	Weak transcription	Osteobl	bone
9	chr2:86088600-86111600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:86089000-86102600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:86089800-86106000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:86089800-86106000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:86090400-86102600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:86090400-86104600	Weak transcription	Liver	Liver
15	chr2:86090600-86109000	Weak transcription	Fetal Stomach	stomach
16	chr2:86090600-86110600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:86091400-86101400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:86092200-86105200	Weak transcription	Right Atrium	heart
19	chr2:86093200-86106200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:86093400-86104600	Weak transcription	Ovary	ovary
21	chr2:86093400-86105800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:86093400-86106200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:86093400-86106800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:86093400-86112400	Weak transcription	Colonic Mucosa	Colon
25	chr2:86093600-86111600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:86093800-86106000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:86093800-86113000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:86094000-86103200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:86094000-86105400	Weak transcription	NH-A	brain
30	chr2:86094400-86101400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:86094800-86101400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:86094800-86105400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:86094800-86106000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:86095000-86102000	Strong transcription	Primary T cells from cord blood	blood
35	chr2:86095000-86103400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:86095200-86102600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:86095200-86102800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:86095400-86104000	Weak transcription	A549	lung
39	chr2:86096200-86108400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:86096800-86107600	Enhancers	Brain Hippocampus Middle	brain
41	chr2:86097000-86104400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:86097200-86100600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:86097200-86102600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:86097400-86102800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:86097600-86102200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:86097600-86102600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:86097600-86102600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:86097600-86103000	Weak transcription	Placenta	Placenta
49	chr2:86097600-86103200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:86097600-86103600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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