Variant report

Variant	rs9858861
Chromosome Location	chr3:156542637-156542638
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156541940-156545935	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:156542437-156542642	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
2	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
3	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:
4	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:
5	chr3:156391796..156394617-chr3:156542307..156544876,4	K562	blood:

No data

Variant related genes	Relation type
LEKR1	TF binding region
ENSG00000243926	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000230457	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10936037	0.85[ASN][1000 genomes]
rs10936038	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10936040	0.82[TSI][hapmap]
rs11711674	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11717133	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12492804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497539	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072896	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086516	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13097325	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13322318	0.82[TSI][hapmap]
rs1384538	0.82[TSI][hapmap]
rs1430410	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1430411	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1560415	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1560416	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1835372	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653817	0.83[YRI][hapmap]
rs344071	0.83[YRI][hapmap]
rs344072	0.83[YRI][hapmap]
rs344074	0.82[YRI][hapmap]
rs4680305	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4680317	0.82[TSI][hapmap]
rs59717073	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776157	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780427	0.82[TSI][hapmap]
rs7618306	0.88[GIH][hapmap]
rs7638625	0.82[TSI][hapmap]
rs7641929	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812169	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9818684	0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs9820830	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837271	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9842198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844054	0.82[TSI][hapmap]
rs9847692	0.88[GIH][hapmap]
rs9871817	0.82[TSI][hapmap]
rs9874866	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]

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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9858861	LINC00886	cis	Stomach	GTEx
rs9858861	LINC00886	cis	Thyroid	GTEx
rs9858861	LINC00886	cis	Nerve Tibial	GTEx
rs9858861	MLF1	cis	parietal	SCAN
rs9858861	Hs.54543	cis	multi-tissue	Pritchard
rs9858861	LINC00886	cis	Esophagus Mucosa	GTEx
rs9858861	LINC00886	cis	Adipose Subcutaneous	GTEx
rs9858861	LINC00886	cis	lung	GTEx
rs9858861		cis	Lymphoblastoid	GTEx
rs9858861	LINC00886	cis	Artery Aorta	GTEx
rs9858861	LINC00886	cis	Artery Tibial	GTEx
rs9858861	LINC00886	cis	Esophagus Muscularis	GTEx
rs9858861	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs9858861	LINC00886	cis	Muscle Skeletal	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
3	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
8	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:156537000-156543400	Weak transcription	Liver	Liver
11	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:156538000-156543400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:156538600-156543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:156538600-156543400	Weak transcription	NHLF	lung
16	chr3:156538800-156543200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:156538800-156543200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:156538800-156543200	Weak transcription	NHDF-Ad	bronchial
19	chr3:156538800-156543400	Weak transcription	HSMMtube	muscle
20	chr3:156539000-156543200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:156539000-156543200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:156539000-156543200	Weak transcription	HMEC	breast
23	chr3:156539000-156543200	Weak transcription	HSMM	muscle
24	chr3:156539000-156543200	Weak transcription	HUVEC	blood vessel
25	chr3:156539000-156543200	Weak transcription	Osteobl	bone
26	chr3:156539000-156543400	Weak transcription	NH-A	brain
27	chr3:156539200-156543200	Weak transcription	GM12878-XiMat	blood
28	chr3:156539200-156543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:156541600-156543000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:156541800-156543200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:156541800-156543400	Enhancers	Fetal Intestine Large	intestine
32	chr3:156541800-156543600	Enhancers	Fetal Intestine Small	intestine
33	chr3:156541800-156543800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:156542000-156542800	Enhancers	Stomach Mucosa	stomach
35	chr3:156542000-156543400	Enhancers	NHEK	skin
36	chr3:156542200-156543200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:156542200-156543400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:156542200-156543400	Enhancers	A549	lung
39	chr3:156542400-156542800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:156542400-156543000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:156542400-156543200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:156542400-156543200	Enhancers	Hela-S3	cervix
43	chr3:156542400-156543200	Enhancers	K562	blood
44	chr3:156542400-156543600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:156542600-156543000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:156542600-156543400	Enhancers	Duodenum Mucosa	Duodenum

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