Variant report

Variant	rs2036963
Chromosome Location	chr9:98230545-98230546
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	chr9:98214310..98216415-chr9:98227721..98230889,3	MCF-7	breast:
2	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10512249	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909892	0.87[EUR][1000 genomes]
rs16909898	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909902	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909904	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909922	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805155	0.87[EUR][1000 genomes]
rs2282040	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282041	0.87[EUR][1000 genomes]
rs2282043	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372566	0.87[EUR][1000 genomes]
rs28377268	0.85[EUR][1000 genomes]
rs28418339	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427480	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28446116	0.87[EUR][1000 genomes]
rs28446321	0.93[EUR][1000 genomes]
rs28448271	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457693	0.86[EUR][1000 genomes]
rs28474857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493225	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494679	0.87[EUR][1000 genomes]
rs28510415	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28520225	0.87[EUR][1000 genomes]
rs28535536	0.87[EUR][1000 genomes]
rs28583690	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28673156	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706464	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780573	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824488	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149656	0.87[EUR][1000 genomes]
rs59015093	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59925771	0.95[EUR][1000 genomes]
rs60150206	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60417486	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867452	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv531634	chr9:98227972-98230831	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2036963	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
4	chr9:98225600-98234000	Weak transcription	Right Atrium	heart
5	chr9:98225800-98239600	Weak transcription	HMEC	breast
6	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
9	chr9:98226000-98251000	Weak transcription	Osteobl	bone
10	chr9:98226200-98232400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr9:98226200-98238400	Weak transcription	NH-A	brain
12	chr9:98226200-98239000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:98226200-98239400	Weak transcription	NHEK	skin
14	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
15	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:98226400-98232200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:98226400-98232400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:98226400-98232600	Strong transcription	Fetal Kidney	kidney
20	chr9:98226400-98232600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr9:98226400-98234200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:98226400-98239200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:98226400-98239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
26	chr9:98226600-98239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:98226600-98239200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:98226600-98239400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:98226800-98230600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:98226800-98232400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr9:98226800-98232600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:98226800-98239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
40	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
42	chr9:98227200-98231200	Strong transcription	Gastric	stomach
43	chr9:98227200-98232000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:98227200-98232200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:98227200-98232600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:98227200-98239200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:98227400-98232200	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links