Variant report

Variant	rs11871969
Chromosome Location	chr17:45992622-45992623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45981534..45985192-chr17:45991810..45993717,3	MCF-7	breast:
2	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
3	chr17:45985387..45988064-chr17:45989640..45992704,3	MCF-7	breast:
4	chr17:45991986..45994660-chr17:45998582..46001397,3	K562	blood:
5	chr17:45991270..45994231-chr17:46005074..46007219,2	K562	blood:
6	chr17:45991808..45994318-chr17:46045941..46048411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11079799	1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11649750	0.86[EUR][1000 genomes]
rs16948424	1.00[YRI][hapmap]
rs17617010	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2074185	1.00[JPT][hapmap]
rs2325714	0.88[EUR][1000 genomes]
rs4793688	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4794224	1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4794318	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60123006	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067380	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6503897	0.85[EUR][1000 genomes]
rs8071778	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11871969	SCRN2	cis	Esophagus Mucosa	GTEx
rs11871969	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs11871969	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
3	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
4	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
6	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
11	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
14	chr17:45980200-46001800	Weak transcription	K562	blood
15	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
19	chr17:45982600-45992800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:45982800-45993000	Weak transcription	NHEK	skin
22	chr17:45983000-45993800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:45983200-45993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:45983200-45995200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:45983200-45995200	Weak transcription	HUVEC	blood vessel
28	chr17:45983200-46000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:45983200-46001200	Weak transcription	A549	lung
30	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
31	chr17:45983400-45992800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
33	chr17:45983600-45992800	Weak transcription	Esophagus	oesophagus
34	chr17:45984000-45993600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:45984200-45993200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:45984200-46000600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:45984400-45993400	Weak transcription	Pancreas	Pancrea
38	chr17:45984600-45993200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:45984600-45994200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:45984800-45992800	Weak transcription	Placenta	Placenta
41	chr17:45985600-45992800	Weak transcription	Lung	lung
42	chr17:45985600-45993200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr17:45985600-45993400	Weak transcription	Fetal Lung	lung
44	chr17:45985600-45993800	Weak transcription	NHLF	lung
45	chr17:45985600-46000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:45985800-45992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:45985800-45992800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr17:45985800-45993000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr17:45985800-45993800	Weak transcription	Brain Angular Gyrus	brain
50	chr17:45985800-45993800	Weak transcription	Brain Cingulate Gyrus	brain

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