Variant report

Variant	rs10476660
Chromosome Location	chr5:95196028-95196029
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:95195981-95196598	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:95194418-95196405	Hela-S3	cervix:	n/a	n/a
3	SMARCC1	chr5:95193756-95196313	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:95193203-95198379	IMR90	lung:	n/a	n/a
5	USF2	chr5:95195999-95196076	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:95194009-95198385	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr5:95195887-95196440	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:95195783-95196394	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:95193934-95201037	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr5:95194460-95196248	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:95193696-95201073	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr5:95194409-95196282	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95194068..95196070-chr5:95401310..95403656,2	K562	blood:
2	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
3	chr5:95195786..95198605-chr5:95296132..95297926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250362	TF binding region
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1004654	0.82[TSI][hapmap]
rs12659828	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465446	0.82[TSI][hapmap]
rs17085209	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2059209	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2059210	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs248340	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs248341	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs6873611	0.87[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6888848	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10476660	SPATA9	cis	cerebellum	SCAN
rs10476660	CHD1	cis	parietal	SCAN
rs10476660	ERAP2	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95192000-95201400	Enhancers	Placenta	Placenta
3	chr5:95192200-95199400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:95192400-95199200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:95193000-95196400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:95193600-95196800	Weak transcription	Right Ventricle	heart
7	chr5:95193800-95196400	Flanking Active TSS	Hela-S3	cervix
8	chr5:95193800-95197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:95194000-95200800	Weak transcription	Gastric	stomach
10	chr5:95194200-95199000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr5:95194600-95196200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:95194600-95196600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:95194600-95197000	Weak transcription	Left Ventricle	heart
15	chr5:95194800-95196200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:95194800-95196800	Weak transcription	Fetal Intestine Large	intestine
17	chr5:95194800-95196800	Weak transcription	Fetal Intestine Small	intestine
18	chr5:95194800-95196800	Weak transcription	Fetal Kidney	kidney
19	chr5:95194800-95197000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:95194800-95197200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:95194800-95199400	Enhancers	Liver	Liver
22	chr5:95195000-95196400	Enhancers	Brain Hippocampus Middle	brain
23	chr5:95195000-95196400	Enhancers	Pancreas	Pancrea
24	chr5:95195000-95196400	Enhancers	Dnd41	blood
25	chr5:95195000-95196600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:95195000-95196600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:95195000-95196600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:95195000-95196800	Weak transcription	Primary T cells from cord blood	blood
29	chr5:95195000-95196800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:95195000-95196800	Enhancers	Adipose Nuclei	Adipose
31	chr5:95195000-95196800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:95195000-95196800	Weak transcription	Fetal Thymus	thymus
33	chr5:95195000-95196800	Enhancers	HSMMtube	muscle
34	chr5:95195000-95196800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr5:95195000-95197000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:95195000-95197000	Weak transcription	Fetal Brain Male	brain
37	chr5:95195000-95197000	Weak transcription	Right Atrium	heart
38	chr5:95195000-95197000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:95195000-95197000	Weak transcription	Stomach Mucosa	stomach
40	chr5:95195000-95197200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:95195000-95197200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr5:95195000-95197200	Weak transcription	Fetal Stomach	stomach
43	chr5:95195000-95197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:95195000-95197600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:95195000-95198400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:95195000-95198400	Weak transcription	Colonic Mucosa	Colon
47	chr5:95195000-95199000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:95195000-95200200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:95195000-95200600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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