Variant report

Variant	rs7556543
Chromosome Location	chr1:186270419-186270420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186268258..186271597-chr1:186273909..186276929,3	MCF-7	breast:
2	chr1:186267939..186270683-chr1:186273055..186275696,2	K562	blood:
3	chr1:186270268..186272079-chr1:186293943..186296923,2	K562	blood:

Variant related genes	Relation type
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10494583	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494584	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406294	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16825150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16825183	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16825185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16825201	0.87[ASN][1000 genomes]
rs16825224	0.87[ASN][1000 genomes]
rs16825243	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16825248	0.87[ASN][1000 genomes]
rs16825279	0.85[ASN][1000 genomes]
rs1919199	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919200	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2273777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297226	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28715477	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3119331	1.00[JPT][hapmap]
rs3131554	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs34585917	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736595	0.87[ASN][1000 genomes]
rs3736597	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3753565	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs3766699	0.83[ASN][1000 genomes]
rs3766702	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs3766703	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3766704	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3766705	0.83[ASN][1000 genomes]
rs3766707	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3820181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3820182	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57040195	0.82[ASN][1000 genomes]
rs6425024	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425027	0.83[ASN][1000 genomes]
rs6425028	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs6664763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6667940	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6679066	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7514615	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7525634	0.83[AMR][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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7556543	CACNA1E	cis	cerebellum	SCAN
rs7556543	OCLM	cis	cerebellum	SCAN
rs7556543	OCLM	cis	parietal	SCAN
rs7556543	C1orf27	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186259600-186273600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:186265200-186271200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:186265600-186279400	Weak transcription	A549	lung
4	chr1:186267200-186271600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:186267200-186281600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:186267400-186271200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:186267400-186280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:186268400-186279200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:186268600-186281200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:186269000-186274800	Weak transcription	Psoas Muscle	Psoas
11	chr1:186269000-186281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:186269200-186270600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:186269400-186277600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:186269400-186281400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:186269400-186281400	Weak transcription	Fetal Heart	heart
16	chr1:186269600-186270600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:186269600-186271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:186269600-186272400	Weak transcription	Thymus	Thymus
19	chr1:186270200-186277400	Enhancers	Primary T cells from cord blood	blood
20	chr1:186270200-186277800	Enhancers	Fetal Thymus	thymus
21	chr1:186270400-186271200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:186270400-186271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:186270400-186271800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr1:186270400-186272400	Genic enhancers	Liver	Liver
25	chr1:186270400-186279200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:186270400-186279600	Enhancers	Primary T helper cells fromperipheralblood	blood

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