Variant report

Variant	rs10496320
Chromosome Location	chr2:86078478-86078479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr2:86078242-86078817	GM12878	blood:	n/a	n/a
2	PML	chr2:86078288-86079120	GM12878	blood:	n/a	n/a
3	FOXM1	chr2:86078258-86078930	GM12878	blood:	n/a	n/a
4	MTA3	chr2:86078255-86079060	GM12878	blood:	n/a	n/a
5	MTA3	chr2:86078221-86078851	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:86078184-86078878	GM12878	blood:	n/a	n/a
7	RUNX3	chr2:86078295-86078913	GM12878	blood:	n/a	n/a
8	YY1	chr2:86078449-86078749	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:86078425-86078579	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ST3GAL5	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10865480	0.83[ASN][1000 genomes]
rs11127003	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127004	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127006	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127007	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11127008	0.88[ASN][1000 genomes]
rs11127009	0.88[ASN][1000 genomes]
rs11694145	0.86[AMR][1000 genomes]
rs12614498	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12618873	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622987	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12990400	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs13014421	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13014890	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13016226	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13033743	0.92[AMR][1000 genomes]
rs1543972	0.84[JPT][hapmap]
rs17026675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1878898	0.84[JPT][hapmap]
rs1878904	0.84[JPT][hapmap]
rs1878905	0.88[ASN][1000 genomes]
rs2280312	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2577768	0.84[JPT][hapmap]
rs2577769	0.84[JPT][hapmap]
rs2679710	0.84[JPT][hapmap]
rs2679711	0.84[JPT][hapmap]
rs2679712	0.84[JPT][hapmap]
rs2679713	0.84[JPT][hapmap]
rs3770097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810821	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832016	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4832210	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4832217	0.84[JPT][hapmap]
rs56049132	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56083339	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62147537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62147538	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62147540	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547636	0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6547640	0.88[ASN][1000 genomes]
rs6720161	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6735629	0.84[JPT][hapmap]
rs6750686	0.89[ASN][1000 genomes]
rs6751743	0.88[ASN][1000 genomes]
rs72842060	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72842061	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558479	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572209	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572386	1.00[YRI][hapmap]
rs7587003	0.88[ASN][1000 genomes]
rs764471	0.84[JPT][hapmap]
rs954176	0.84[JPT][hapmap]
rs959313	0.84[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10496320	MRPL35	cis	parietal	SCAN
rs10496320	C2orf51	cis	cerebellum	SCAN
rs10496320	IMMT	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86055000-86080000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:86055200-86080400	Weak transcription	Colonic Mucosa	Colon
3	chr2:86063800-86080200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:86065200-86080000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:86065400-86079400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:86065600-86078600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:86066000-86080600	Weak transcription	Small Intestine	intestine
8	chr2:86066000-86106200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:86066200-86081400	Weak transcription	Right Ventricle	heart
10	chr2:86066400-86091400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:86067000-86099000	Weak transcription	Gastric	stomach
12	chr2:86067200-86087000	Weak transcription	Fetal Brain Male	brain
13	chr2:86067400-86080400	Weak transcription	Left Ventricle	heart
14	chr2:86067400-86084800	Weak transcription	Ovary	ovary
15	chr2:86067600-86078600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:86067600-86078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:86067600-86086200	Weak transcription	Fetal Brain Female	brain
18	chr2:86067800-86080000	Weak transcription	K562	blood
19	chr2:86069400-86080400	Weak transcription	Stomach Mucosa	stomach
20	chr2:86070600-86078600	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:86070800-86080200	Weak transcription	HUVEC	blood vessel
22	chr2:86071000-86080600	Weak transcription	Fetal Intestine Large	intestine
23	chr2:86071200-86079400	Strong transcription	Dnd41	blood
24	chr2:86071400-86080800	Weak transcription	Fetal Intestine Small	intestine
25	chr2:86071800-86078600	Strong transcription	Thymus	Thymus
26	chr2:86071800-86080800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:86071800-86096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:86072000-86090400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:86072000-86096800	Weak transcription	Psoas Muscle	Psoas
30	chr2:86072200-86080000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:86072800-86079400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:86073000-86083600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:86073800-86078600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:86074000-86089800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:86074200-86078800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:86074400-86078600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:86074600-86078800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:86074600-86079200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:86074600-86080000	Weak transcription	HSMMtube	muscle
40	chr2:86074600-86080800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:86074600-86089600	Weak transcription	NH-A	brain
42	chr2:86074800-86086200	Weak transcription	HSMM	muscle
43	chr2:86075200-86082400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:86075400-86079200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:86075400-86080000	Weak transcription	Pancreas	Pancrea
46	chr2:86075400-86114000	Weak transcription	Aorta	Aorta
47	chr2:86076000-86090400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:86076800-86078600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr2:86076800-86078600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:86076800-86078800	Strong transcription	A549	lung

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