Variant report

Variant	rs10858002
Chromosome Location	chr1:114082932-114082933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114082118..114084710-chr1:114087135..114089127,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10745339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs10858000	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs10858001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10858005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10858007	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs10858008	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs10858011	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs11102648	0.96[ASN][1000 genomes]
rs11102649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11102651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs11102653	0.95[ASN][1000 genomes]
rs11102654	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11102657	0.85[ASN][1000 genomes]
rs11102658	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102661	0.87[ASN][1000 genomes]
rs11102669	0.86[ASN][1000 genomes]
rs1113523	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1146182	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1146187	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12021513	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs12037873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12039224	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12043639	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074958	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs12077419	0.94[ASN][1000 genomes]
rs1217192	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1217193	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1217199	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1217200	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1217201	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1217203	0.90[ASN][1000 genomes]
rs1217204	0.90[ASN][1000 genomes]
rs1217208	0.90[ASN][1000 genomes]
rs1217210	0.87[ASN][1000 genomes]
rs1217211	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1217214	0.89[ASN][1000 genomes]
rs1217215	0.90[ASN][1000 genomes]
rs1217221	0.83[ASN][1000 genomes]
rs1217223	0.90[ASN][1000 genomes]
rs1217226	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs1217227	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs1217228	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs1217230	0.90[ASN][1000 genomes]
rs1217232	0.90[ASN][1000 genomes]
rs1217233	0.90[ASN][1000 genomes]
rs1217234	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1217235	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1217236	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.90[ASN][1000 genomes]
rs1217237	0.90[ASN][1000 genomes]
rs1228280	0.87[ASN][1000 genomes]
rs1230655	0.86[ASN][1000 genomes]
rs1230656	0.80[ASN][1000 genomes]
rs1230658	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1230659	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1230661	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1230663	0.80[ASN][1000 genomes]
rs1230671	0.87[ASN][1000 genomes]
rs1235687	0.92[ASN][1000 genomes]
rs1235688	0.90[ASN][1000 genomes]
rs1237289	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12565589	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1343125	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs1343128	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1343629	0.81[LWK][hapmap]
rs1418957	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418958	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17013326	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs17031716	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1743605	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1777234	0.87[ASN][1000 genomes]
rs1777237	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1777238	0.86[ASN][1000 genomes]
rs1777241	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2153977	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2636002	0.82[ASN][1000 genomes]
rs2798135	0.87[ASN][1000 genomes]
rs2798138	0.87[ASN][1000 genomes]
rs2884703	0.93[ASN][1000 genomes]
rs2884704	0.87[ASN][1000 genomes]
rs4259646	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs4274063	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4456089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs4838997	0.86[ASN][1000 genomes]
rs4839335	0.82[ASN][1000 genomes]
rs6537790	0.86[YRI][hapmap]
rs6537792	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6689879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704188	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72687973	0.86[ASN][1000 genomes]
rs72687980	0.94[ASN][1000 genomes]
rs7536360	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7554019	0.81[LWK][hapmap];0.86[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	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv946153	chr1:114080236-114088844	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10858002	PHTF1	cis	cerebellum	SCAN
rs10858002	DENND2C	cis	parietal	SCAN
rs10858002	MAGI3	cis	cerebellum	SCAN
rs10858002	BCL2L15	cis	cerebellum	SCAN
rs10858002	MAGI3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
2	chr1:114077600-114083000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:114077800-114083000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:114077800-114084400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:114077800-114084400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:114077800-114084400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:114078000-114090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:114078600-114084200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:114078600-114084600	Weak transcription	HSMMtube	muscle
10	chr1:114079200-114083200	Weak transcription	Osteobl	bone
11	chr1:114079400-114084400	Weak transcription	NH-A	brain
12	chr1:114080000-114084400	Weak transcription	NHLF	lung
13	chr1:114080200-114083000	Weak transcription	Ovary	ovary
14	chr1:114080600-114088600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:114081400-114083000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:114081400-114084800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:114081600-114084200	Weak transcription	NHEK	skin
18	chr1:114081600-114084400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:114081600-114084400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:114081600-114084800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:114082400-114083200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:114082400-114088400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:114082600-114084800	Enhancers	Fetal Intestine Large	intestine
24	chr1:114082600-114084800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:114082600-114100400	Weak transcription	Fetal Kidney	kidney
26	chr1:114082800-114083200	Enhancers	Pancreas	Pancrea
27	chr1:114082800-114083200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:114082800-114083200	Flanking Active TSS	NHDF-Ad	bronchial
29	chr1:114082800-114083400	Enhancers	Liver	Liver
30	chr1:114082800-114084600	Enhancers	HepG2	liver
31	chr1:114082800-114085000	Enhancers	Stomach Mucosa	stomach
32	chr1:114082800-114085600	Enhancers	HMEC	breast

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