Variant report

Variant	rs2952294
Chromosome Location	chr17:66451708-66451709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66030471..66033206-chr17:66450900..66454415,3	MCF-7	breast:
2	chr17:66286038..66290193-chr17:66450658..66456945,10	MCF-7	breast:
3	chr17:66242276..66246117-chr17:66451301..66455927,10	MCF-7	breast:
4	chr17:66416176..66417821-chr17:66449194..66452011,2	MCF-7	breast:
5	chr17:65820769..65822418-chr17:66451010..66453920,2	MCF-7	breast:
6	chr17:66435049..66438436-chr17:66449646..66452604,3	K562	blood:
7	chr17:66435631..66438436-chr17:66449646..66452604,2	K562	blood:

Variant related genes	Relation type
ENSG00000171634	Chromatin interaction
ENSG00000182481	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000196704	Chromatin interaction
ENSG00000265100	Chromatin interaction
ENSG00000141337	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11868680	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1808335	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111508	0.85[ASN][1000 genomes]
rs2302783	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909207	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs2909209	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2909211	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2909213	0.83[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909216	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909217	0.88[ASN][1000 genomes]
rs2909218	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs2909220	0.84[ASN][1000 genomes]
rs2909221	0.83[ASN][1000 genomes]
rs2952279	0.88[TSI][hapmap]
rs2952286	0.82[ASN][1000 genomes]
rs2952289	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2952290	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2952295	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952296	0.94[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6501468	0.89[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs71378928	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8072338	0.89[EUR][1000 genomes]
rs883541	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2952294	CD79B	cis	cerebellum	SCAN
rs2952294	STRADA	cis	parietal	SCAN
rs2952294	TANC2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:66420800-66451800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:66425400-66452000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr17:66432200-66452400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:66433000-66451800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr17:66433000-66451800	Weak transcription	Hela-S3	cervix
7	chr17:66434800-66452200	Weak transcription	Dnd41	blood
8	chr17:66434800-66452400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:66434800-66452600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:66435200-66452200	Weak transcription	Stomach Mucosa	stomach
11	chr17:66437600-66452800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:66438000-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:66438200-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr17:66438200-66452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:66438200-66452400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:66438400-66452400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr17:66438400-66452400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:66443200-66452200	Weak transcription	Fetal Brain Female	brain
19	chr17:66443800-66452200	Weak transcription	Fetal Brain Male	brain
20	chr17:66446000-66451800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:66446800-66452800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:66447000-66451800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:66447000-66452000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:66447000-66452400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr17:66447200-66451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr17:66447200-66451800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:66447200-66452000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:66447200-66452400	Weak transcription	Pancreas	Pancrea
29	chr17:66447200-66452400	Weak transcription	Spleen	Spleen
30	chr17:66447400-66452000	Weak transcription	Aorta	Aorta
31	chr17:66447800-66452400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:66447800-66452600	Weak transcription	Gastric	stomach
33	chr17:66448000-66452000	Weak transcription	Brain Angular Gyrus	brain
34	chr17:66448000-66452000	Weak transcription	Brain Anterior Caudate	brain
35	chr17:66448000-66452000	Weak transcription	HUVEC	blood vessel
36	chr17:66448000-66452200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:66448000-66452400	Weak transcription	Esophagus	oesophagus
38	chr17:66448000-66452400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:66448000-66452400	Weak transcription	Fetal Stomach	stomach
40	chr17:66448000-66452600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr17:66448200-66451800	Weak transcription	Brain Substantia Nigra	brain
42	chr17:66448200-66452000	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:66448200-66452000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:66448400-66451800	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:66448400-66452000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr17:66448600-66452000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:66448800-66452400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr17:66449000-66452200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr17:66449200-66452400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr17:66449400-66451800	Weak transcription	Primary hematopoietic stem cells	blood

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