Variant report

Variant	rs2207189
Chromosome Location	chr1:171388916-171388917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10798394	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798395	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912911	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11579231	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12072674	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12121150	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12126686	0.90[ASN][1000 genomes]
rs12402699	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402708	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689514	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72637249	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv470745	chr1:171381746-171409514	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv465628	chr1:171381746-171409515	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv548189	chr1:171381746-171409515	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2207189	SELP	cis	parietal	SCAN
rs2207189	CD247	cis	parietal	SCAN
rs2207189	TBX19	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171383200-171390800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:171383400-171389600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:171387000-171389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:171388000-171389800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:171388000-171390800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:171388000-171391000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:171388400-171389600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:171388400-171389600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:171388400-171389600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:171388400-171390200	Enhancers	Placenta	Placenta
11	chr1:171388600-171389000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:171388600-171391200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:171388800-171390200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:171388800-171390400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:171388800-171391000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:171388800-171391400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:171388800-171394600	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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