Variant report

Variant	rs2659101
Chromosome Location	chr19:51322211-51322212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51314145..51316152-chr19:51321518..51323994,2	MCF-7	breast:
2	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
3	chr19:51316544..51318313-chr19:51321412..51323624,2	K562	blood:
4	chr19:51317914..51322870-chr19:51325257..51328084,4	MCF-7	breast:
5	chr19:51322195..51323768-chr19:51333223..51335759,2	K562	blood:
6	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:
7	chr19:51321294..51329149-chr19:51334672..51341529,13	K562	blood:

Variant related genes	Relation type
ENSG00000174562	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000167747	Chromatin interaction
ENSG00000167748	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1054713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672844	0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs197589	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1978605	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2247289	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2411334	0.95[ASN][1000 genomes]
rs2434449	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2456584	0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2456585	0.86[ASN][1000 genomes]
rs2560931	0.86[ASN][1000 genomes]
rs2560933	0.86[ASN][1000 genomes]
rs2560934	0.87[CEU][hapmap];0.89[GIH][hapmap]
rs2659058	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2659059	0.88[ASN][1000 genomes]
rs2659099	0.96[ASN][1000 genomes]
rs2659100	0.98[ASN][1000 genomes]
rs2659103	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659104	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs266114	0.87[CEU][hapmap]
rs266116	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs266122	0.86[ASN][1000 genomes]
rs266123	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs266125	0.86[ASN][1000 genomes]
rs266127	0.86[ASN][1000 genomes]
rs266128	0.82[ASN][1000 genomes]
rs5516	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs788886	0.87[ASN][1000 genomes]
rs788887	0.88[ASN][1000 genomes]
rs788889	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs788890	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs788891	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv516450	chr19:51321083-51322312	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv524637	chr19:51321083-51332670	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv523089	chr19:51321083-51336197	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2659101	HSPBP1	cis	parietal	SCAN
rs2659101	ZNF784	cis	parietal	SCAN
rs2659101	ZNF418	cis	parietal	SCAN
rs2659101	NCRNA00085	cis	parietal	SCAN
rs2659101	MYADM	cis	cerebellum	SCAN
rs2659101	NLRP13	cis	parietal	SCAN
rs2659101	KLK1	cis	lymphoblastoid	seeQTL
rs2659101	KLK1	cis	multi-tissue	Pritchard
rs2659101	KLK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51320800-51338800	Weak transcription	Right Atrium	heart
2	chr19:51321200-51322600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr19:51321400-51322400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
4	chr19:51321400-51322400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr19:51321400-51322800	Flanking Active TSS	Pancreas	Pancrea
6	chr19:51321400-51324000	Flanking Active TSS	GM12878-XiMat	blood
7	chr19:51321600-51322400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr19:51321600-51322400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
9	chr19:51321600-51322400	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr19:51321800-51322400	Bivalent Enhancer	Esophagus	oesophagus
11	chr19:51321800-51322800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:51321800-51323400	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr19:51321800-51327600	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:51322000-51322400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
15	chr19:51322000-51322400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr19:51322000-51322400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:51322000-51323200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr19:51322000-51323200	Enhancers	Primary B cells from cord blood	blood
19	chr19:51322200-51322400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:51322200-51322400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
21	chr19:51322200-51322400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr19:51322200-51322400	Flanking Active TSS	Spleen	Spleen
23	chr19:51322200-51323000	Enhancers	K562	blood
24	chr19:51322200-51323400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:51322200-51323400	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr19:51322200-51324400	Bivalent/Poised TSS	Colonic Mucosa	Colon

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