Variant report

Variant	rs11534279
Chromosome Location	chr9:96401464-96401465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96347655..96349520-chr9:96399670..96402056,2	K562	blood:
2	chr9:96328888..96330785-chr9:96400006..96401542,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10761245	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10761246	0.89[ASN][1000 genomes]
rs10761247	0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap]
rs10761249	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10761250	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10821184	0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs10821185	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10821186	0.87[EUR][1000 genomes]
rs10821187	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821188	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821189	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821190	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10821191	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10821192	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10821193	0.83[EUR][1000 genomes]
rs10821194	0.83[EUR][1000 genomes]
rs10821195	0.82[EUR][1000 genomes]
rs10821196	0.83[CHB][hapmap]
rs10992807	0.83[CHB][hapmap]
rs10992812	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs10992813	0.84[EUR][1000 genomes]
rs10992815	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10992819	0.86[EUR][1000 genomes]
rs10992829	0.83[EUR][1000 genomes]
rs10992831	0.83[EUR][1000 genomes]
rs10992839	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10992840	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10992842	0.83[EUR][1000 genomes]
rs10992854	0.82[CHB][hapmap]
rs10992860	0.81[CEU][hapmap]
rs1132004	0.92[CEU][hapmap]
rs11793637	0.91[CHB][hapmap];0.87[GIH][hapmap]
rs12002044	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12238738	0.89[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs1806458	0.83[CHB][hapmap]
rs1806524	0.85[CEU][hapmap]
rs2001315	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001589	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001610	0.92[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2398848	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2398849	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2398855	0.86[CHB][hapmap]
rs2398856	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34103739	0.82[EUR][1000 genomes]
rs35171420	0.83[EUR][1000 genomes]
rs3750354	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750357	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3750358	0.83[CHB][hapmap]
rs3750359	0.89[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs3750362	0.83[CHB][hapmap]
rs3829758	0.82[EUR][1000 genomes]
rs6479499	0.83[CHB][hapmap]
rs6479504	0.85[EUR][1000 genomes]
rs7024028	0.83[CHB][hapmap]
rs7036592	0.83[EUR][1000 genomes]
rs7040340	0.92[CEU][hapmap]
rs7044244	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7849752	0.95[CHB][hapmap]
rs7851178	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7851271	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7864397	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7868191	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11534279	PTCH1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
3	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:96390200-96405400	Weak transcription	HepG2	liver
5	chr9:96391600-96402000	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:96391800-96402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:96391800-96402400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:96391800-96402400	Strong transcription	Placenta	Placenta
9	chr9:96392000-96403400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:96392200-96402200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr9:96392200-96402200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr9:96392200-96403800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr9:96392200-96412000	Weak transcription	HMEC	breast
14	chr9:96392200-96423600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:96392400-96402600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:96392400-96402600	Strong transcription	Liver	Liver
17	chr9:96393200-96402800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:96393600-96406600	Weak transcription	GM12878-XiMat	blood
19	chr9:96396400-96402200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr9:96396400-96412000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:96397200-96407800	Weak transcription	NHEK	skin
22	chr9:96397400-96402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:96398000-96402400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:96398000-96403400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:96398200-96402200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:96398200-96402600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr9:96398200-96411200	Weak transcription	HUVEC	blood vessel
28	chr9:96398200-96413800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:96398400-96402400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr9:96398400-96403200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:96398600-96403000	ZNF genes & repeats	Fetal Brain Female	brain
32	chr9:96398800-96402800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:96398800-96402800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr9:96399000-96402400	Strong transcription	Osteobl	bone
35	chr9:96399000-96423400	Strong transcription	Fetal Intestine Large	intestine
36	chr9:96399200-96406200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:96399400-96401800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:96399400-96402000	Weak transcription	Lung	lung
39	chr9:96399400-96402800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:96399400-96405400	Weak transcription	Esophagus	oesophagus
41	chr9:96399400-96423600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr9:96399600-96402800	Strong transcription	Fetal Kidney	kidney
43	chr9:96399600-96403200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:96399800-96402400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
45	chr9:96400000-96401800	Weak transcription	Small Intestine	intestine
46	chr9:96400000-96402000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:96400000-96402800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:96400000-96403600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr9:96400000-96405400	Weak transcription	Right Ventricle	heart
50	chr9:96400000-96405400	Weak transcription	NHLF	lung

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