Variant report

Variant	rs572055
Chromosome Location	chr13:30516268-30516269
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	chr13:30513452..30517431-chr13:30524367..30526986,3	MCF-7	breast:
2	chr13:30494281..30495981-chr13:30514922..30517429,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-90M5.1.1-1	chr13:30516234-30516704	ENSG00000122043.6

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10467438	1.00[ASN][1000 genomes]
rs11147402	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11147403	0.83[ASN][1000 genomes]
rs11619001	1.00[ASN][1000 genomes]
rs11619980	1.00[ASN][1000 genomes]
rs11620184	1.00[ASN][1000 genomes]
rs3803269	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3803271	1.00[ASN][1000 genomes]
rs475607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486677	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503693	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs531084	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548941	1.00[ASN][1000 genomes]
rs562459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565264	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs567291	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs571307	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573132	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584801	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs585231	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs586146	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs586167	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs588372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs602388	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602884	1.00[ASN][1000 genomes]
rs605464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618877	1.00[ASN][1000 genomes]
rs619367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632258	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633496	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646983	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647794	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];1.00[ASN][1000 genomes]
rs651873	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662224	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs669105	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679603	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs716801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73159307	1.00[ASN][1000 genomes]
rs7338743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7358963	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7996122	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818606	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs818607	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs818608	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs865324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866019	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912785	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285067	1.00[ASN][1000 genomes]
rs9285068	1.00[ASN][1000 genomes]
rs9578150	1.00[ASN][1000 genomes]
rs9579497	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9579501	1.00[ASN][1000 genomes]
rs9579505	1.00[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	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
2	chr13:30512400-30518400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:30513000-30517200	Weak transcription	Primary T cells from cord blood	blood
4	chr13:30514000-30517600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr13:30514000-30518000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:30514000-30522600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:30514200-30517200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:30514400-30516400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:30514800-30516400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:30515200-30518000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:30515400-30517000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr13:30515600-30517200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr13:30515800-30516400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:30515800-30517000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr13:30515800-30517800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:30516000-30516600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell

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