Variant report

Variant	rs4847409
Chromosome Location	chr1:93795932-93795933
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:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93794370..93796630-chr1:93807088..93808805,2	K562	blood:
2	chr1:93793661..93797290-chr1:93805926..93809295,5	MCF-7	breast:
3	chr1:93779027..93781639-chr1:93793756..93796548,2	K562	blood:
4	chr1:93793462..93796127-chr1:93796578..93799399,2	MCF-7	breast:
5	chr1:93795727..93797402-chr1:93804546..93806225,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMED5-1	chr1:93792580-93803825	NONHSAT004520
2	lnc-DR1-1	chr1:93795119-93796358	XLOC_000294

No data

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1000606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10430073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782958	0.97[EUR][1000 genomes]
rs10782959	0.87[YRI][hapmap]
rs1081523	0.86[EUR][1000 genomes]
rs1081524	0.88[EUR][1000 genomes]
rs1081525	0.89[EUR][1000 genomes]
rs1081526	0.89[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10874771	0.97[EUR][1000 genomes]
rs10874774	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10874775	0.92[EUR][1000 genomes]
rs1088319	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164878	0.80[EUR][1000 genomes]
rs11164882	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11164888	0.98[EUR][1000 genomes]
rs11164889	0.98[EUR][1000 genomes]
rs11164890	0.98[EUR][1000 genomes]
rs11164891	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582703	0.97[EUR][1000 genomes]
rs11584466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799928	1.00[JPT][hapmap]
rs11800760	1.00[JPT][hapmap]
rs11801175	1.00[JPT][hapmap]
rs11802420	1.00[JPT][hapmap]
rs11807404	1.00[JPT][hapmap]
rs11808445	1.00[JPT][hapmap]
rs12070900	0.84[CEU][hapmap];0.97[EUR][1000 genomes]
rs12071627	0.97[EUR][1000 genomes]
rs12080715	0.96[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12088338	0.82[EUR][1000 genomes]
rs12090723	0.97[EUR][1000 genomes]
rs12731675	0.97[EUR][1000 genomes]
rs12731809	0.97[EUR][1000 genomes]
rs1323626	0.88[EUR][1000 genomes]
rs1323627	0.87[EUR][1000 genomes]
rs1323628	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs1414367	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs1535698	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17131699	0.96[TSI][hapmap]
rs2031223	0.92[EUR][1000 genomes]
rs2031224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104280	0.96[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap]
rs2749735	0.80[EUR][1000 genomes]
rs2783492	0.80[EUR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2783506	0.80[EUR][1000 genomes]
rs2815409	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs2815410	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs2815411	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2815413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2815414	0.84[EUR][1000 genomes]
rs3171	1.00[JPT][hapmap]
rs41528947	1.00[JPT][hapmap]
rs4573531	0.97[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4847407	0.97[EUR][1000 genomes]
rs4847411	0.92[EUR][1000 genomes]
rs485622	0.89[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs505531	0.83[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs508942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs519723	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs523262	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs546	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs556888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs558667	0.96[EUR][1000 genomes]
rs559397	0.97[EUR][1000 genomes]
rs56303209	0.97[EUR][1000 genomes]
rs566743	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs571212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs573056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs581825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs587754	0.97[EUR][1000 genomes]
rs589241	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs605759	0.90[EUR][1000 genomes]
rs615416	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629153	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs631966	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633789	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs637198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs641390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541348	1.00[JPT][hapmap]
rs6541351	0.93[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs6541360	1.00[JPT][hapmap]
rs6541400	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658178	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs661566	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs662546	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6657587	0.98[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6667540	1.00[JPT][hapmap]
rs6667701	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6671070	1.00[JPT][hapmap]
rs667680	0.84[EUR][1000 genomes]
rs6679304	1.00[JPT][hapmap]
rs6687359	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6701250	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs6704067	1.00[JPT][hapmap]
rs670650	0.96[EUR][1000 genomes]
rs671559	0.83[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs698926	0.90[EUR][1000 genomes]
rs7413775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518171	1.00[JPT][hapmap]
rs7519163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525189	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529230	1.00[JPT][hapmap]
rs7529639	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7532015	0.91[ASN][1000 genomes]
rs7534543	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7545358	1.00[JPT][hapmap]
rs7546661	0.89[EUR][1000 genomes]
rs7551635	0.97[EUR][1000 genomes]
rs7555292	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs771448	0.87[EUR][1000 genomes]
rs771449	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771450	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771451	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771452	0.89[EUR][1000 genomes]
rs771453	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771456	0.91[EUR][1000 genomes]
rs771457	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771460	0.90[EUR][1000 genomes]
rs771463	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771464	0.92[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs771467	0.89[EUR][1000 genomes]
rs771468	0.89[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs771471	0.89[EUR][1000 genomes]
rs771472	0.89[EUR][1000 genomes]
rs771474	0.89[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes]
rs771480	0.89[EUR][1000 genomes]
rs797660	0.84[EUR][1000 genomes]
rs797669	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs809515	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs810028	0.89[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8489	1.00[JPT][hapmap]
rs8561	1.00[JPT][hapmap]
rs9432680	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9432700	0.97[EUR][1000 genomes]
rs9432701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4847409	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs4847409	LOC646848	cis	normal skin	skin_eQTL
rs4847409	RP4-717I23.3	cis	lung	GTEx
rs4847409	LOC646848	cis	multi-tissue	Pritchard
rs4847409	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs4847409	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs4847409	RP4-717I23.3	cis	Artery Aorta	GTEx
rs4847409	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs4847409	TMED5	cis	parietal	SCAN
rs4847409	RP4-717I23.3	cis	Stomach	GTEx
rs4847409	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs4847409	RP4-717I23.3	cis	Whole Blood	GTEx
rs4847409	TMED5	cis	multi-tissue	Pritchard
rs4847409	DR1	cis	multi-tissue	Pritchard
rs4847409	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs4847409	RP4-717I23.3	cis	Thyroid	GTEx
rs4847409	RP4-717I23.3	cis	Artery Tibial	GTEx
rs4847409	TMED5	cis	cerebellum	SCAN
rs4847409	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93753000-93803600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:93753200-93806400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:93755400-93802600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:93755400-93803200	Weak transcription	Fetal Thymus	thymus
5	chr1:93755600-93803400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:93755600-93804200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:93755800-93801400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:93756000-93803800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:93765800-93809800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:93767800-93801400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:93768600-93803000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:93772600-93806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:93779600-93804000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:93783000-93803400	Weak transcription	Left Ventricle	heart
15	chr1:93783800-93801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:93784400-93804000	Weak transcription	Thymus	Thymus
17	chr1:93786200-93803800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:93789000-93797200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:93789000-93803800	Weak transcription	Placenta	Placenta
20	chr1:93789200-93810200	Weak transcription	Esophagus	oesophagus
21	chr1:93789600-93800400	Weak transcription	Primary T cells from cord blood	blood
22	chr1:93789600-93806600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:93790400-93800200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:93790600-93804600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:93790800-93803400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:93790800-93810000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:93791000-93801600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:93791000-93802200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:93791200-93802800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:93791200-93803800	Weak transcription	A549	lung
31	chr1:93791800-93797200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:93791800-93797200	Weak transcription	Stomach Mucosa	stomach
33	chr1:93793600-93796000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:93794000-93796000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:93794400-93810600	Weak transcription	Fetal Brain Male	brain
36	chr1:93794600-93804000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:93794600-93806400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:93794800-93796000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:93794800-93796800	Weak transcription	Osteobl	bone
40	chr1:93794800-93797000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:93794800-93802600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:93794800-93804000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:93794800-93804600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:93795000-93796000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:93795000-93796600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:93795000-93797000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:93795000-93797200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr1:93795000-93801400	Weak transcription	HSMMtube	muscle
49	chr1:93795000-93802800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:93795000-93803200	Weak transcription	Duodenum Mucosa	Duodenum

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