Variant report

Variant	rs1400964
Chromosome Location	chr1:223534949-223534950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223533339..223535356-chr1:223536427..223538674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10907375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11261268	0.87[ASN][1000 genomes]
rs11261269	0.88[ASN][1000 genomes]
rs11579995	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12064476	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12074609	0.81[ASN][1000 genomes]
rs12074782	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12078619	0.87[ASN][1000 genomes]
rs12082133	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12087387	0.86[ASN][1000 genomes]
rs12094897	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12405882	0.88[ASN][1000 genomes]
rs1547789	0.94[EUR][1000 genomes]
rs1621030	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17162005	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163834	0.94[EUR][1000 genomes]
rs17163836	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1914612	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282399	0.94[EUR][1000 genomes]
rs2298063	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2353204	0.88[ASN][1000 genomes]
rs2678369	0.80[CHB][hapmap];0.87[GIH][hapmap]
rs2678370	0.81[GIH][hapmap]
rs28788929	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28897212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34482638	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35059272	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35345617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35727959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35736338	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35996176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs41460051	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4661241	0.94[EUR][1000 genomes]
rs59584296	0.88[ASN][1000 genomes]
rs61838203	0.87[ASN][1000 genomes]
rs61838204	0.87[ASN][1000 genomes]
rs61838211	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61838232	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61838233	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61838244	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61838245	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6604707	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6661314	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677044	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6679661	0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6682552	0.80[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6689850	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6700523	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701453	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs825148	0.80[CHB][hapmap];0.81[GIH][hapmap]
rs862216	0.87[ASN][1000 genomes]
rs866637	0.80[CHB][hapmap];0.87[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223514400-223535800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:223528000-223535000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:223528000-223536400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:223531200-223536400	Weak transcription	Psoas Muscle	Psoas
5	chr1:223533800-223536400	Weak transcription	Esophagus	oesophagus
6	chr1:223534600-223535800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:223534600-223536400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:223534800-223535000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
9	chr1:223534800-223535000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:223534800-223535000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:223534800-223535200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr1:223534800-223535600	Bivalent Enhancer	Primary T cells from cord blood	blood
13	chr1:223534800-223536400	Enhancers	Primary T helper cells PMA-I stimulated	--

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