Variant report

Variant	rs12659828
Chromosome Location	chr5:95196856-95196857
allele	C/T
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	chr5:95196808-95199477	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:95196678-95199527	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr5:95196856-95197979	Hela-S3	cervix:	n/a	n/a
4	GTF2F1	chr5:95196769-95198157	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr5:95196744-95198555	IMR90	lung:	n/a	n/a
6	POLR2A	chr5:95193203-95198379	IMR90	lung:	n/a	n/a
7	POLR2A	chr5:95196791-95197725	U87	brain:	n/a	n/a
8	USF2	chr5:95196778-95198596	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:95196492-95199509	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:95196795-95199552	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr5:95196827-95198137	Hela-S3	cervix:	n/a	chr5:95197239-95197250 chr5:95197241-95197252 chr5:95197239-95197252
12	POLR2A	chr5:95194009-95198385	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr5:95196772-95197691	A549	lung:	n/a	n/a
14	POLR2A	chr5:95193934-95201037	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:95196743-95199555	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:95193696-95201073	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr5:95196803-95198812	Hela-S3	cervix:	n/a	chr5:95198034-95198045
18	POLR2A	chr5:95196738-95198538	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr5:95196844-95197970	MCF-7	breast:	n/a	chr5:95197239-95197250 chr5:95197241-95197252 chr5:95197239-95197252
20	POLR2A	chr5:95196785-95197822	U87	brain:	n/a	n/a
21	MYBL2	chr5:95196851-95197512	HepG2	liver:	n/a	n/a
22	MYC	chr5:95196812-95198170	Hela-S3	cervix:	n/a	chr5:95198034-95198045

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
2	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: 2 )

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

rs_ID	r²[population]
rs1004654	0.88[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10476660	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	0.88[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs17085209	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2059209	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs2059210	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs248340	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]
rs248341	0.84[CHD][hapmap]
rs6873611	0.88[TSI][hapmap]
rs6888848	0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12659828	SPATA9	cis	cerebellum	SCAN
rs12659828	CHD1	cis	parietal	SCAN

Chromatin state (count:102 , 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	chr5:95193800-95197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:95194000-95200800	Weak transcription	Gastric	stomach
7	chr5:95194200-95199000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:95194600-95197000	Weak transcription	Left Ventricle	heart
10	chr5:95194800-95197000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:95194800-95197200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:95194800-95199400	Enhancers	Liver	Liver
13	chr5:95195000-95197000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:95195000-95197000	Weak transcription	Fetal Brain Male	brain
15	chr5:95195000-95197000	Weak transcription	Right Atrium	heart
16	chr5:95195000-95197000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:95195000-95197000	Weak transcription	Stomach Mucosa	stomach
18	chr5:95195000-95197200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:95195000-95197200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:95195000-95197200	Weak transcription	Fetal Stomach	stomach
21	chr5:95195000-95197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:95195000-95197600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:95195000-95198400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:95195000-95198400	Weak transcription	Colonic Mucosa	Colon
25	chr5:95195000-95199000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:95195000-95200200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:95195000-95200600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:95195000-95208400	Weak transcription	Ovary	ovary
30	chr5:95195200-95197600	Weak transcription	Brain Angular Gyrus	brain
31	chr5:95195200-95198800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:95195200-95199000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:95195200-95200600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:95195200-95217400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:95195400-95197000	Enhancers	HUVEC	blood vessel
36	chr5:95195400-95199200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr5:95195400-95199200	Enhancers	NHEK	skin
38	chr5:95195400-95201600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:95195600-95197000	Weak transcription	Lung	lung
40	chr5:95195600-95197000	Enhancers	A549	lung
41	chr5:95195600-95197200	Enhancers	HepG2	liver
42	chr5:95195600-95198800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:95195600-95198800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:95195600-95199000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:95195600-95199000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:95195600-95206200	Weak transcription	Brain Anterior Caudate	brain
47	chr5:95195800-95197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:95195800-95197000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:95195800-95197800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr5:95195800-95198000	Weak transcription	Aorta	Aorta

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