Variant report

Variant	rs10873710
Chromosome Location	chr1:86072216-86072217
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:86045532..86047930-chr1:86071624..86075132,3	MCF-7	breast:
2	chr1:86071869..86072512-chr1:86157974..86158600,3	MCF-7	breast:
3	chr1:86050411..86052188-chr1:86071339..86074227,2	MCF-7	breast:
4	chr1:86071671..86072280-chr1:86095942..86096727,2	MCF-7	breast:
5	chr1:86044508..86046493-chr1:86071384..86074227,2	K562	blood:
6	chr1:86044046..86050058-chr1:86065602..86074449,16	MCF-7	breast:
7	chr1:86044508..86046201-chr1:86070309..86072884,2	K562	blood:
8	chr1:86067788..86069598-chr1:86069646..86072509,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1047892	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap]
rs1047895	0.93[ASW][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs10782553	0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873709	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1094359	0.81[ASN][1000 genomes]
rs11161641	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11161643	0.93[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11161645	0.86[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11578464	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128916	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1764285	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1764291	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1764292	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1764299	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1775988	0.93[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs1775990	0.81[CHB][hapmap]
rs1928626	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2389969	0.85[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2389970	0.93[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2785081	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2995537	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs34448540	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs373787	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs414618	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs418979	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4370804	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs4949911	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4949912	0.82[AFR][1000 genomes]
rs4949915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs709801	0.81[ASN][1000 genomes]
rs7532758	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs821386	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs821389	0.93[ASW][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs821393	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs821394	0.81[ASN][1000 genomes]
rs821396	0.81[ASN][1000 genomes]
rs843969	0.81[ASN][1000 genomes]
rs952837	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9658595	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10873710	LOC339524	cis	cerebellum	SCAN
rs10873710	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs10873710	STRA8	trans	parietal	SCAN
rs10873710	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86064000-86072600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:86068000-86074600	Enhancers	Fetal Intestine Small	intestine
5	chr1:86068400-86072400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:86068400-86074800	Enhancers	Fetal Intestine Large	intestine
7	chr1:86069000-86072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:86070000-86076800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:86070600-86076600	Weak transcription	Fetal Stomach	stomach
10	chr1:86070800-86072600	Enhancers	HepG2	liver
11	chr1:86071200-86076600	Weak transcription	Fetal Lung	lung
12	chr1:86071200-86076800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:86071400-86072600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:86071400-86072600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:86071400-86072600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:86071400-86072600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:86071400-86073200	Enhancers	Pancreas	Pancrea
18	chr1:86071400-86074200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:86071400-86074200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:86071400-86075000	Enhancers	HSMM	muscle
21	chr1:86071400-86075400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:86071600-86072600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:86071600-86073400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:86071600-86074400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:86071600-86074600	Enhancers	HUVEC	blood vessel
26	chr1:86071600-86076600	Enhancers	NHDF-Ad	bronchial
27	chr1:86071600-86078800	Enhancers	NHLF	lung
28	chr1:86071800-86073400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:86071800-86073400	Enhancers	Osteobl	bone
30	chr1:86071800-86074200	Enhancers	NHEK	skin
31	chr1:86071800-86074400	Enhancers	HMEC	breast
32	chr1:86071800-86074400	Enhancers	NH-A	brain
33	chr1:86071800-86074600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:86071800-86074600	Enhancers	HSMMtube	muscle
35	chr1:86071800-86076800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:86072000-86072800	Weak transcription	Fetal Kidney	kidney
37	chr1:86072000-86072800	Weak transcription	Small Intestine	intestine
38	chr1:86072000-86073200	Enhancers	A549	lung
39	chr1:86072000-86073800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:86072000-86074000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:86072000-86074200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:86072000-86074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:86072000-86074200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr1:86072000-86074200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:86072000-86074400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:86072000-86074400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:86072000-86074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:86072200-86073000	Enhancers	Hela-S3	cervix
49	chr1:86072200-86073200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:86072200-86073600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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