Variant report

Variant	rs11891096
Chromosome Location	chr2:86275698-86275699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10779967	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11885520	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12473739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13390107	1.00[ASN][1000 genomes]
rs13420958	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1469982	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1559513	1.00[JPT][hapmap]
rs2059353	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2288117	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311561	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311565	0.82[CEU][hapmap]
rs311567	0.82[CEU][hapmap]
rs311569	0.82[CEU][hapmap]
rs311570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311571	0.82[CEU][hapmap]
rs311572	0.82[CEU][hapmap]
rs311573	0.82[CEU][hapmap]
rs311580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311584	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311586	0.89[AFR][1000 genomes]
rs34892520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810828	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4832027	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4832028	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832239	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832254	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4832258	1.00[JPT][hapmap]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6547666	1.00[JPT][hapmap]
rs6707736	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6715623	1.00[ASN][1000 genomes]
rs6720431	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6749218	1.00[ASN][1000 genomes]
rs6752561	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6758535	1.00[JPT][hapmap]
rs72847843	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7558040	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7565645	1.00[JPT][hapmap]
rs7583021	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs889911	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs918856	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929916	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679308	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs979940	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11891096	POLR1A	cis	Nerve Tibial	GTEx
rs11891096	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs11891096	MRPL35	cis	Artery Aorta	GTEx
rs11891096	MRPL35	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr2:86251200-86283000	Strong transcription	HepG2	liver
3	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
12	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
14	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:86264400-86285400	Strong transcription	A549	lung
16	chr2:86265200-86281600	Strong transcription	HMEC	breast
17	chr2:86265200-86284000	Strong transcription	NHEK	skin
18	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
20	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
21	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:86265600-86282000	Strong transcription	K562	blood
24	chr2:86265600-86282400	Strong transcription	Brain Germinal Matrix	brain
25	chr2:86265600-86289800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:86265800-86276600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr2:86265800-86278600	Weak transcription	Small Intestine	intestine
28	chr2:86265800-86280400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:86265800-86284000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:86266000-86276600	Strong transcription	Brain Hippocampus Middle	brain
32	chr2:86266000-86278000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr2:86266000-86281800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:86266000-86282600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:86266000-86282800	Strong transcription	Gastric	stomach
36	chr2:86266000-86282800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:86266000-86283800	Strong transcription	Fetal Intestine Small	intestine
38	chr2:86266000-86287800	Weak transcription	Right Atrium	heart
39	chr2:86266200-86280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:86266200-86281000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:86266200-86281400	Strong transcription	NHLF	lung
42	chr2:86266200-86281600	Strong transcription	Osteobl	bone
43	chr2:86266200-86282200	Strong transcription	GM12878-XiMat	blood
44	chr2:86266200-86282800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:86266200-86282800	Strong transcription	Fetal Stomach	stomach
46	chr2:86266200-86284600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:86266400-86275800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr2:86266400-86277000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr2:86266400-86278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:86266400-86281400	Strong transcription	Liver	Liver

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