Variant report

Variant	rs6587625
Chromosome Location	chr1:151820324-151820325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151818078..151821727-chr1:151829199..151833455,4	MCF-7	breast:
2	chr1:151817401..151820382-chr1:151830495..151832320,2	MCF-7	breast:
3	chr1:151567685..151569478-chr1:151820200..151821930,2	MCF-7	breast:
4	chr1:151817773..151822675-chr1:151880093..151884786,6	K562	blood:
5	chr1:151819170..151821882-chr1:151830861..151833145,2	K562	blood:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1056037	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs1129117	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12567049	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12727170	0.90[CHD][hapmap]
rs16833584	0.90[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16833599	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16833604	0.94[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279503	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs2879130	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60166269	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815147	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587622	0.81[CHB][hapmap]
rs745055	0.81[ASN][1000 genomes]
rs7524706	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536659	0.83[JPT][hapmap]
rs7544269	0.83[JPT][hapmap]
rs7556386	0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[ASN][1000 genomes]
rs923547	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923548	0.86[YRI][hapmap]
rs998500	0.86[ASN][1000 genomes]
rs998501	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6587625	S100A10	cis	cerebellum	SCAN
rs6587625	THEM4	cis	lymphoblastoid	seeQTL
rs6587625	THEM4	cis	cerebellum	SCAN
rs6587625	OTUD7B	cis	cerebellum	SCAN
rs6587625	S100A10	cis	lymphoblastoid	seeQTL
rs6587625	NPR1	cis	parietal	SCAN
rs6587625	THEM4	cis	parietal	SCAN
rs6587625	PLEKHO1	cis	cerebellum	SCAN
rs6587625	SELENBP1	cis	parietal	SCAN
rs6587625	LCE2C	cis	cerebellum	SCAN
rs6587625	C1orf230	cis	cerebellum	SCAN
rs6587625	S100A14	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151812800-151820600	Weak transcription	Right Atrium	heart
2	chr1:151813400-151821200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:151813400-151828600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:151814000-151820800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:151814800-151827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:151818200-151820800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:151818400-151824400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:151818600-151820600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151818600-151820800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:151818600-151821000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:151819000-151820400	Weak transcription	Fetal Lung	lung
12	chr1:151819200-151820400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:151819200-151820400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:151819200-151820800	Weak transcription	HSMMtube	muscle
15	chr1:151819200-151825200	Weak transcription	Gastric	stomach
16	chr1:151819200-151827200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
18	chr1:151819400-151820400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:151819400-151820600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:151819400-151820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:151819400-151820800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:151819400-151820800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:151819400-151821800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:151819800-151821400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:151820000-151825800	Weak transcription	Hela-S3	cervix
26	chr1:151820200-151821000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:151820200-151821800	Enhancers	HUVEC	blood vessel

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