Variant report

Variant	rs17639286
Chromosome Location	chr19:36520765-36520766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36515922..36517591-chr19:36519314..36521673,2	K562	blood:
2	chr19:36518073..36521044-chr19:36525057..36527255,2	K562	blood:
3	chr19:36520595..36521436-chr19:36541888..36542480,3	MCF-7	breast:
4	chr19:36499646..36502624-chr19:36517798..36521500,4	MCF-7	breast:
5	chr19:36518180..36521030-chr19:36528618..36530229,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181392	Chromatin interaction
ENSG00000105270	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10407011	0.87[EUR][1000 genomes]
rs10414877	0.86[EUR][1000 genomes]
rs10420353	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10421966	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10423651	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10425692	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12462432	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12462632	0.86[EUR][1000 genomes]
rs12462674	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs12972490	0.96[EUR][1000 genomes]
rs12976505	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12976812	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs12977814	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12978482	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12981654	0.96[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12984982	1.00[ASW][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];1.00[MKK][hapmap]
rs2023865	0.92[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2142075	1.00[LWK][hapmap]
rs2239510	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs35125548	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35875194	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3826995	0.92[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4461192	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs71337524	0.90[EUR][1000 genomes]
rs721542	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7259592	0.85[EUR][1000 genomes]
rs7260609	0.86[EUR][1000 genomes]
rs8103569	0.92[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
6	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17639286	ATXN7L1	trans	parietal	SCAN
rs17639286	ZNF229	cis	parietal	SCAN
rs17639286	SHKBP1	cis	cerebellum	SCAN
rs17639286	CYP2B7P1	cis	parietal	SCAN
rs17639286	ZNF345	cis	parietal	SCAN
rs17639286	GRIK5	cis	cerebellum	SCAN
rs17639286	PSG9	cis	cerebellum	SCAN
rs17639286	CCDC97	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36505600-36521000	Weak transcription	Fetal Brain Male	brain
2	chr19:36505800-36522000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:36505800-36522200	Weak transcription	Fetal Kidney	kidney
4	chr19:36505800-36522800	Weak transcription	Small Intestine	intestine
5	chr19:36506000-36522400	Weak transcription	NH-A	brain
6	chr19:36506000-36522800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:36506000-36523000	Weak transcription	HSMM	muscle
8	chr19:36506000-36523200	Weak transcription	Left Ventricle	heart
9	chr19:36506000-36523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:36506200-36522400	Strong transcription	Fetal Stomach	stomach
11	chr19:36506200-36522800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:36506200-36523000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:36506200-36523200	Weak transcription	HUVEC	blood vessel
14	chr19:36506200-36523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:36506200-36523400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:36506400-36521600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:36506400-36521800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:36506400-36523000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
20	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
22	chr19:36507600-36521800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:36508800-36532400	Weak transcription	NHEK	skin
24	chr19:36511400-36521800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:36513400-36523600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:36513600-36523000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:36513600-36525600	Weak transcription	K562	blood
28	chr19:36514400-36522400	Weak transcription	Liver	Liver
29	chr19:36514400-36523200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr19:36515000-36522800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr19:36515000-36523200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:36515200-36522800	Weak transcription	NHDF-Ad	bronchial
33	chr19:36515200-36523000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:36515400-36523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:36515400-36523200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:36515400-36523200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:36515400-36523600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
40	chr19:36515600-36520800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr19:36515600-36523200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:36515600-36523400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:36515800-36523200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:36515800-36523400	Weak transcription	Primary B cells from cord blood	blood
45	chr19:36516200-36523600	Weak transcription	Gastric	stomach
46	chr19:36516400-36522800	Weak transcription	Colon Smooth Muscle	Colon
47	chr19:36516400-36523200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr19:36516800-36522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:36517000-36522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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