Variant report

Variant	rs7952989
Chromosome Location	chr12:58095989-58095990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58095878..58097507-chr12:58102658..58104994,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1027315	0.85[EUR][1000 genomes]
rs1038914	0.90[JPT][hapmap]
rs1050045	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172304	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12826708	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12826985	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564374	0.90[JPT][hapmap]
rs1633359	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2270777	0.92[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap]
rs2277324	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2277326	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs2307097	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs238516	0.82[MKK][hapmap]
rs238517	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs701007	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7134861	0.81[EUR][1000 genomes]
rs7138608	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304145	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311632	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966795	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs799265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs799267	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903067	0.90[JPT][hapmap]
rs923828	0.88[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv508676	chr12:58045136-58098538	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	esv1820402	chr12:58092554-58110211	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7952989	KRT8	cis	cerebellum	SCAN
rs7952989	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs7952989	FAM119B	cis	lymphoblastoid	seeQTL
rs7952989	KRT75	cis	cerebellum	SCAN
rs7952989	STAT6	cis	parietal	SCAN
rs7952989	TENC1	cis	cerebellum	SCAN
rs7952989	FAM119B	cis	cerebellum	SCAN
rs7952989	NCKAP1L	cis	parietal	SCAN
rs7952989	TSPAN31	cis	cerebellum	SCAN
rs7952989	OR6C4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58088800-58097800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr12:58088800-58099400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:58088800-58099400	Weak transcription	Small Intestine	intestine
4	chr12:58089000-58097000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:58089000-58109400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:58089000-58110000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:58089200-58096800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:58089200-58097200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:58089200-58097200	Weak transcription	Stomach Mucosa	stomach
10	chr12:58089200-58097600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:58089200-58097600	Weak transcription	HMEC	breast
12	chr12:58089200-58103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:58089200-58115400	Weak transcription	Fetal Heart	heart
14	chr12:58089400-58096200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:58089400-58096600	Strong transcription	Primary T cells from cord blood	blood
16	chr12:58089400-58096800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:58089600-58096400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:58089600-58097400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:58089600-58098600	Weak transcription	Hela-S3	cervix
20	chr12:58089800-58101200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:58090200-58096400	Weak transcription	Psoas Muscle	Psoas
22	chr12:58090200-58098800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:58091000-58109800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:58091000-58110200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:58091200-58097200	Weak transcription	K562	blood
26	chr12:58091200-58101200	Weak transcription	Colonic Mucosa	Colon
27	chr12:58091200-58109600	Weak transcription	Right Ventricle	heart
28	chr12:58091200-58116600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:58091400-58097200	Weak transcription	NHEK	skin
30	chr12:58091400-58108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:58091400-58110200	Weak transcription	HUVEC	blood vessel
32	chr12:58091400-58111600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:58091600-58097600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:58091800-58097200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:58092200-58096600	Weak transcription	NHDF-Ad	bronchial
36	chr12:58092200-58097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:58092200-58106600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:58092400-58096000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:58092400-58096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:58092400-58096800	Weak transcription	Osteobl	bone
41	chr12:58092400-58097000	Weak transcription	Brain Substantia Nigra	brain
42	chr12:58092600-58096000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:58092600-58096200	Weak transcription	Dnd41	blood
44	chr12:58092600-58096800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:58092600-58097000	Weak transcription	Thymus	Thymus
46	chr12:58092600-58097600	Weak transcription	Fetal Kidney	kidney
47	chr12:58092600-58099400	Weak transcription	Lung	lung
48	chr12:58092600-58103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:58092600-58106400	Weak transcription	Aorta	Aorta
50	chr12:58092600-58106600	Weak transcription	Esophagus	oesophagus

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