Variant report

Variant	rs818608
Chromosome Location	chr13:30513052-30513053
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	chr13:30512486..30516242-chr13:30529306..30532066,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10467438	0.83[ASN][1000 genomes]
rs11147402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11147403	1.00[ASN][1000 genomes]
rs11619001	0.83[ASN][1000 genomes]
rs11619980	0.83[ASN][1000 genomes]
rs11620184	0.83[ASN][1000 genomes]
rs3803269	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3803271	0.83[ASN][1000 genomes]
rs475607	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4769781	0.81[TSI][hapmap]
rs485057	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs486677	0.83[ASN][1000 genomes]
rs503693	0.82[MEX][hapmap]
rs531084	0.83[ASN][1000 genomes]
rs548941	0.83[ASN][1000 genomes]
rs562459	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs565264	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571307	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs572055	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs573132	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs584801	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585231	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586167	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588372	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs602388	0.83[ASN][1000 genomes]
rs602884	0.83[ASN][1000 genomes]
rs605464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs605478	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs618877	0.83[ASN][1000 genomes]
rs619367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs632214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs632258	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs633496	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs646983	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs647794	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs651873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs662224	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669105	0.83[ASN][1000 genomes]
rs716801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73159307	0.83[ASN][1000 genomes]
rs7338743	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7358963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7996122	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs818606	1.00[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818607	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865324	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs866019	0.83[ASN][1000 genomes]
rs912785	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9285067	0.83[ASN][1000 genomes]
rs9285068	0.83[ASN][1000 genomes]
rs9578150	0.83[ASN][1000 genomes]
rs9579497	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9579501	0.83[ASN][1000 genomes]
rs9579505	0.83[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs818608	RNF6	cis	parietal	SCAN
rs818608	ATP5EP2	cis	parietal	SCAN
rs818608	FAM123A	cis	cerebellum	SCAN
rs818608	MTIF3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30509800-30515000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:30510400-30515000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
5	chr13:30511600-30513400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr13:30511600-30514000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr13:30511600-30514400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:30511600-30514800	Weak transcription	Liver	Liver
9	chr13:30511800-30514400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr13:30512000-30513200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:30512200-30514200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:30512400-30513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr13:30512400-30513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:30512400-30514000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr13:30512400-30514200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr13:30512400-30518400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:30512600-30513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr13:30512600-30513800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr13:30512800-30515800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr13:30513000-30514000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr13:30513000-30514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr13:30513000-30517200	Weak transcription	Primary T cells from cord blood	blood

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