Variant report

Variant	rs1453379
Chromosome Location	chr8:95970239-95970240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95961511..95965084-chr8:95968441..95972141,5	K562	blood:
2	chr8:95960008..95964622-chr8:95970124..95974538,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INTS8-4	chr8:95970223-95970407	NONHSAT127811

Variant related genes	Relation type
ENSG00000164938	Chromatin interaction
ENSG00000253878	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10081596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10086284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10098778	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10099941	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10104909	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10112447	0.94[ASN][1000 genomes]
rs1011795	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1011796	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10429294	0.85[AFR][1000 genomes]
rs10429443	0.91[AFR][1000 genomes]
rs10441538	0.84[CHB][hapmap]
rs10956929	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10956930	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10956931	1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs10956932	1.00[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1129152	0.86[CHB][hapmap]
rs11784717	0.85[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11996455	0.86[CHB][hapmap]
rs12545596	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12548999	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12549003	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679044	0.85[CHB][hapmap]
rs13255935	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13257021	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13266313	0.91[AFR][1000 genomes]
rs13271375	0.86[CHB][hapmap]
rs13278601	0.83[AFR][1000 genomes]
rs13281625	0.91[AFR][1000 genomes]
rs13281709	0.91[AFR][1000 genomes]
rs1349763	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1453377	0.94[ASW][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16893776	0.94[ASW][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2013597	0.93[ASN][1000 genomes]
rs2084968	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123647	1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs2340586	0.88[AFR][1000 genomes]
rs28560301	0.90[AFR][1000 genomes]
rs28591375	0.91[AFR][1000 genomes]
rs28716845	0.91[AFR][1000 genomes]
rs2904893	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945554	1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs2956210	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2956216	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs3019175	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs3802193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4582532	0.90[AFR][1000 genomes]
rs4734293	0.91[ASN][1000 genomes]
rs4734294	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4734295	0.81[CHB][hapmap]
rs4735328	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4735331	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4735332	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4735334	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735335	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4735336	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4735337	0.94[ASW][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4735338	0.81[AFR][1000 genomes]
rs4735339	0.88[ASW][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4735340	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs477653	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs550418	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs550564	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs551270	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6471499	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6471500	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6471503	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6471504	0.86[CHB][hapmap]
rs683832	0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs6982393	0.94[ASW][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6983000	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6983948	0.81[AFR][1000 genomes]
rs6987256	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6991067	0.86[CHB][hapmap]
rs6993278	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001535	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7004862	0.86[CHB][hapmap]
rs7005317	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7007935	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7015841	1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7017487	1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs726816	0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7815762	0.85[AFR][1000 genomes]
rs7819800	0.91[AFR][1000 genomes]
rs7820818	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7823059	0.91[AFR][1000 genomes]
rs7823366	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7827478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7835379	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7845219	1.00[CHB][hapmap]
rs896846	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs896847	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs896850	0.93[ASN][1000 genomes]
rs896851	0.92[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs896854	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9297949	0.91[AFR][1000 genomes]
rs9643353	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv818645	chr8:95967838-95974373	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1453379	ESRP1	cis	parietal	SCAN
rs1453379	LAPTM4B	cis	cerebellum	SCAN
rs1453379	TP53INP1	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95962200-95977800	Weak transcription	Hela-S3	cervix
2	chr8:95962400-95971400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr8:95962600-95970600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:95962800-95972400	Weak transcription	Aorta	Aorta
5	chr8:95962800-95974200	Weak transcription	Gastric	stomach
6	chr8:95962800-95975800	Weak transcription	Right Ventricle	heart
7	chr8:95962800-95977000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr8:95962800-95979800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr8:95962800-95980200	Weak transcription	Ovary	ovary
10	chr8:95962800-95980600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:95963000-95971200	Weak transcription	Fetal Intestine Small	intestine
12	chr8:95963000-95971400	Weak transcription	Primary B cells from cord blood	blood
13	chr8:95963000-95975800	Weak transcription	Fetal Stomach	stomach
14	chr8:95963000-95980400	Weak transcription	HSMM	muscle
15	chr8:95963400-95974200	Weak transcription	Psoas Muscle	Psoas
16	chr8:95963600-95971400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr8:95963600-95972400	Weak transcription	NHLF	lung
18	chr8:95963600-95973800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:95963600-95974000	Weak transcription	Esophagus	oesophagus
20	chr8:95963600-95977800	Weak transcription	HUVEC	blood vessel
21	chr8:95963600-95979600	Weak transcription	A549	lung
22	chr8:95963800-95970800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:95963800-95973800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:95963800-95979400	Weak transcription	Colon Smooth Muscle	Colon
25	chr8:95964000-95971000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr8:95964200-95970400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:95964200-95971400	Weak transcription	Fetal Intestine Large	intestine
28	chr8:95964400-95971000	Weak transcription	HMEC	breast
29	chr8:95964400-95972000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:95964400-95973600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr8:95964400-95973800	Weak transcription	Osteobl	bone
32	chr8:95964400-95976000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:95964400-95980000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:95964400-96002200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:95964600-95970400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr8:95964600-95970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr8:95964600-95971000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr8:95964600-95971200	Weak transcription	HepG2	liver
39	chr8:95964600-95972000	Weak transcription	Fetal Lung	lung
40	chr8:95964600-95972000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr8:95964600-95973600	Weak transcription	Lung	lung
42	chr8:95964600-95979400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr8:95964600-95980200	Weak transcription	Brain Substantia Nigra	brain
44	chr8:95964600-95980600	Weak transcription	Fetal Brain Female	brain
45	chr8:95964600-95992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:95964800-95970400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr8:95964800-95970800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr8:95964800-95971000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:95964800-95971200	Weak transcription	Stomach Mucosa	stomach
50	chr8:95964800-95973400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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