Variant report

Variant	rs1128535
Chromosome Location	chr3:49866392-49866393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10049413	0.95[ASN][1000 genomes]
rs1049256	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1062633	0.88[CHB][hapmap]
rs10865958	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865959	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11130214	0.85[ASN][1000 genomes]
rs11130216	0.85[ASN][1000 genomes]
rs11130218	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130219	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130221	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130228	0.81[CHB][hapmap]
rs11709680	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11710675	0.87[ASN][1000 genomes]
rs11714957	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715304	0.98[ASN][1000 genomes]
rs11716575	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11717256	0.99[ASN][1000 genomes]
rs11717463	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11920900	0.88[ASN][1000 genomes]
rs12381242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490656	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13063621	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084243	0.89[ASN][1000 genomes]
rs13085679	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086130	0.89[ASN][1000 genomes]
rs13086465	0.87[ASN][1000 genomes]
rs13090611	0.83[ASN][1000 genomes]
rs1317140	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13316065	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1491986	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799843	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1799845	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2234385	0.96[ASN][1000 genomes]
rs2234391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247036	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276864	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2291542	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2307021	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2352967	0.94[ASN][1000 genomes]
rs2352974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352975	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2353579	0.81[CHB][hapmap]
rs2681780	0.80[CEU][hapmap]
rs2681781	0.80[CEU][hapmap]
rs34451146	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34522271	0.89[ASN][1000 genomes]
rs34614773	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34735338	0.89[ASN][1000 genomes]
rs35210174	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs35261599	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35474403	0.89[ASN][1000 genomes]
rs3749237	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3749240	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3749241	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774733	0.81[CHB][hapmap]
rs3811695	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811696	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3819325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519692	0.89[ASN][1000 genomes]
rs4768	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855841	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855850	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855862	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855867	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57648519	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59906301	0.84[ASN][1000 genomes]
rs60205400	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260715	0.89[ASN][1000 genomes]
rs62260719	0.96[ASN][1000 genomes]
rs62260729	0.95[ASN][1000 genomes]
rs6446295	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6766836	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785549	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804655	0.85[ASN][1000 genomes]
rs695238	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324996	0.84[ASN][1000 genomes]
rs7372725	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372730	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7372966	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374183	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374277	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7426497	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7429353	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431078	0.89[ASN][1000 genomes]
rs7431106	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618501	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618519	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7629936	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7634886	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634902	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649348	1.00[CEU][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814765	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819511	0.93[ASN][1000 genomes]
rs9821675	0.85[CEU][hapmap]
rs9850465	0.93[ASN][1000 genomes]
rs9853458	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9855505	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859153	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9865480	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871654	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872864	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873183	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876508	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882639	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1128535	RBM6	cis	Thyroid	GTEx
rs1128535	RBM6	cis	Esophagus Muscularis	GTEx
rs1128535	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs1128535	RBM6	cis	Nerve Tibial	GTEx
rs1128535	RBM6	cis	Adipose Subcutaneous	GTEx
rs1128535	UBA7	cis	Whole Blood	GTEx
rs1128535	RBM6	cis	lung	GTEx
rs1128535	RBM6	cis	Artery Tibial	GTEx
rs1128535	RBM6	cis	Whole Blood	GTEx
rs1128535	FAM212A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49861400-49866400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:49863400-49876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:49863400-49876800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:49863400-49879000	Weak transcription	Fetal Brain Male	brain
8	chr3:49863600-49866400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:49863600-49866600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:49863600-49866600	Weak transcription	A549	lung
11	chr3:49863600-49868000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49863600-49868400	Weak transcription	Hela-S3	cervix
13	chr3:49863600-49868800	Weak transcription	K562	blood
14	chr3:49863600-49876600	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:49863800-49867200	Weak transcription	Fetal Lung	lung
16	chr3:49863800-49874000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:49863800-49875600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:49863800-49879000	Weak transcription	NH-A	brain
19	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:49864000-49876600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
22	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
23	chr3:49864200-49866600	Weak transcription	HMEC	breast
24	chr3:49864200-49873000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:49864200-49876800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:49864400-49876800	Weak transcription	Brain Anterior Caudate	brain
28	chr3:49864600-49866600	Weak transcription	Ovary	ovary
29	chr3:49864600-49876800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:49864600-49882000	Weak transcription	Osteobl	bone
31	chr3:49864800-49872800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:49864800-49878000	Strong transcription	Fetal Thymus	thymus
33	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49865000-49866400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:49865000-49866800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:49865000-49867800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:49865000-49869800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:49865000-49870800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:49865000-49872400	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:49865000-49872800	Strong transcription	Fetal Stomach	stomach
42	chr3:49865000-49876400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49865000-49876400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:49865000-49886000	Strong transcription	Dnd41	blood
45	chr3:49865200-49866400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:49865200-49869000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:49865200-49872000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:49865200-49872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:49865200-49872400	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr3:49865200-49872800	Strong transcription	Fetal Intestine Small	intestine

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