Variant report

Variant	rs7295422
Chromosome Location	chr12:58099736-58099737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58098435..58100959-chr12:58118325..58121297,2	K562	blood:
2	chr12:57995985..57998083-chr12:58098335..58100355,2	K562	blood:
3	chr12:58087405..58089121-chr12:58098744..58101715,3	MCF-7	breast:
4	chr12:58098671..58101243-chr12:58113313..58115696,2	K562	blood:
5	chr12:58098442..58100613-chr12:58118455..58121698,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135506	Chromatin interaction
ENSG00000257342	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000255737	Chromatin interaction

Extended variants
information (count: 29 )
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];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172304	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12826708	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12826985	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564374	0.90[JPT][hapmap]
rs1633359	0.92[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	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs701007	0.94[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];0.92[AMR][1000 genomes];0.98[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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952989	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs799267	0.91[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:4 , 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	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
4	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
rs7295422	KRT8	cis	cerebellum	SCAN
rs7295422	KRT75	cis	cerebellum	SCAN
rs7295422	OR6C4	cis	cerebellum	SCAN
rs7295422	NCKAP1L	cis	parietal	SCAN
rs7295422	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs7295422	FAM119B	cis	lymphoblastoid	seeQTL
rs7295422	FAM119B	cis	cerebellum	SCAN
rs7295422	TENC1	cis	cerebellum	SCAN
rs7295422	STAT6	cis	parietal	SCAN
rs7295422	TSPAN31	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58089000-58109400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:58089000-58110000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:58089200-58103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:58089200-58115400	Weak transcription	Fetal Heart	heart
5	chr12:58089800-58101200	Strong transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:58091000-58109800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:58091000-58110200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:58091200-58101200	Weak transcription	Colonic Mucosa	Colon
9	chr12:58091200-58109600	Weak transcription	Right Ventricle	heart
10	chr12:58091200-58116600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:58091400-58108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:58091400-58110200	Weak transcription	HUVEC	blood vessel
13	chr12:58091400-58111600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:58092200-58106600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:58092600-58103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:58092600-58106400	Weak transcription	Aorta	Aorta
17	chr12:58092600-58106600	Weak transcription	Esophagus	oesophagus
18	chr12:58092600-58107600	Weak transcription	Pancreas	Pancrea
19	chr12:58092800-58109000	Weak transcription	HSMMtube	muscle
20	chr12:58092800-58109200	Weak transcription	HepG2	liver
21	chr12:58092800-58109400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:58093000-58106600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:58093400-58106400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:58093400-58109600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:58093400-58115400	Weak transcription	Fetal Brain Male	brain
26	chr12:58093600-58109000	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:58094400-58106400	Weak transcription	Spleen	Spleen
28	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:58094600-58101000	Weak transcription	Gastric	stomach
30	chr12:58095400-58100000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:58095400-58101400	Strong transcription	Fetal Lung	lung
32	chr12:58095400-58103000	Strong transcription	Liver	Liver
33	chr12:58095600-58102400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:58095800-58101600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:58096000-58100600	Strong transcription	Placenta	Placenta
36	chr12:58096000-58101600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:58096000-58102200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:58096200-58102800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:58096400-58100200	Strong transcription	Brain Anterior Caudate	brain
40	chr12:58096600-58101200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:58096600-58109200	Weak transcription	Brain Angular Gyrus	brain
42	chr12:58096800-58100600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:58096800-58110200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:58097000-58100200	Strong transcription	Brain Germinal Matrix	brain
45	chr12:58097000-58100400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:58097200-58116200	Weak transcription	Psoas Muscle	Psoas
47	chr12:58097400-58101400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:58097400-58109200	Weak transcription	Brain Substantia Nigra	brain
49	chr12:58097400-58109800	Weak transcription	NHEK	skin
50	chr12:58097600-58101400	Strong transcription	Stomach Smooth Muscle	stomach

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