Variant report

Variant	rs7161611
Chromosome Location	chr14:20831406-20831407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:20823483..20825949-chr14:20830269..20832448,2	MCF-7	breast:
2	chr14:20809956..20813449-chr14:20829422..20833018,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259001	Chromatin interaction
ENSG00000129484	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10129957	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10130660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10147163	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10148359	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12323412	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12323610	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12891805	0.86[EUR][1000 genomes]
rs2297616	0.90[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2700	0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs3093882	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3093890	0.90[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3093897	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3093902	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3093904	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3093907	0.82[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap]
rs3093933	0.85[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3093939	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs3093942	0.81[CEU][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34848586	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4415933	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4981150	0.81[CEU][hapmap]
rs4981158	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981983	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4981998	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57101853	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58530849	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59821173	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6575135	0.81[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs8009242	0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs8014147	0.82[EUR][1000 genomes]
rs8022565	0.81[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs878157	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs884368	0.81[CEU][hapmap]
rs9323870	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7161611	ZNF219	cis	cerebellum	SCAN
rs7161611	PARP2	cis	multi-tissue	Pritchard
rs7161611	PARP2	cis	cerebellum	SCAN
rs7161611	PARP2	cis	parietal	SCAN
rs7161611	RPPH1	cis	multi-tissue	Pritchard
rs7161611	PRMT5	cis	parietal	SCAN
rs7161611	JUB	cis	cerebellum	SCAN
rs7161611	TTC5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:20812600-20831800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:20812600-20834600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:20812600-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:20812600-20845600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:20813200-20831600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr14:20813200-20869200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:20823200-20834600	Weak transcription	Small Intestine	intestine
9	chr14:20824600-20840800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:20824800-20836000	Weak transcription	Psoas Muscle	Psoas
11	chr14:20824800-20836200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:20824800-20839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:20825000-20836600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr14:20825000-20836800	Weak transcription	Stomach Mucosa	stomach
15	chr14:20825200-20834600	Weak transcription	Aorta	Aorta
16	chr14:20825200-20863200	Weak transcription	Fetal Heart	heart
17	chr14:20825400-20834200	Weak transcription	Colonic Mucosa	Colon
18	chr14:20825400-20834800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr14:20825800-20832400	Weak transcription	Lung	lung
20	chr14:20825800-20834600	Weak transcription	Right Ventricle	heart
21	chr14:20825800-20837400	Weak transcription	Fetal Kidney	kidney
22	chr14:20825800-20846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:20826000-20834000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr14:20826000-20834000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:20826000-20834200	Weak transcription	Thymus	Thymus
26	chr14:20826000-20834400	Weak transcription	Spleen	Spleen
27	chr14:20826000-20834600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr14:20826000-20836000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:20826200-20832400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:20826200-20834000	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:20826200-20839000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:20826200-20841400	Weak transcription	K562	blood
33	chr14:20826400-20834000	Weak transcription	NHLF	lung
34	chr14:20826400-20834200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr14:20826400-20834200	Weak transcription	Fetal Lung	lung
36	chr14:20826400-20836600	Weak transcription	Brain Substantia Nigra	brain
37	chr14:20826400-20836800	Weak transcription	Brain Angular Gyrus	brain
38	chr14:20826400-20847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr14:20826600-20833000	Weak transcription	Left Ventricle	heart
40	chr14:20826600-20833800	Weak transcription	NHEK	skin
41	chr14:20826600-20834200	Weak transcription	Fetal Thymus	thymus
42	chr14:20826600-20834200	Weak transcription	GM12878-XiMat	blood
43	chr14:20826600-20834400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr14:20826600-20834400	Weak transcription	HMEC	breast
45	chr14:20826600-20836000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:20826600-20836200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr14:20826600-20840800	Weak transcription	Fetal Brain Male	brain
48	chr14:20826800-20832400	Weak transcription	Primary B cells from cord blood	blood
49	chr14:20826800-20832400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr14:20826800-20832400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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