Variant report

Variant	rs664026
Chromosome Location	chr9:136824023-136824024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136819142..136821965-chr9:136822895..136826242,3	K562	blood:
2	chr9:136822394..136827953-chr9:136855901..136860268,9	MCF-7	breast:
3	chr9:136734394..136737190-chr9:136823584..136826132,2	MCF-7	breast:
4	chr9:136821303..136824220-chr9:136826571..136828241,2	MCF-7	breast:
5	chr9:136821904..136824368-chr9:136852633..136855112,2	MCF-7	breast:
6	chr9:136823911..136827460-chr9:136829913..136836528,5	MCF-7	breast:
7	chr9:136817340..136820147-chr9:136822604..136825397,2	MCF-7	breast:
8	chr9:136815263..136820961-chr9:136821414..136825553,6	MCF-7	breast:
9	chr9:136737400..136743457-chr9:136819359..136829756,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1633759	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16767	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16803	0.93[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16819	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256875	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256876	0.82[EUR][1000 genomes]
rs2810536	0.83[ASN][1000 genomes]
rs503376	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520308	0.91[JPT][hapmap];0.89[MEX][hapmap]
rs557500	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636667	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637521	0.85[EUR][1000 genomes]
rs654182	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs681492	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs681508	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682388	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682418	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694505	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv982642	chr9:136819005-136837069	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2761297	chr9:136819288-136825744	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs664026	TOR1B	cis	parietal	SCAN
rs664026	GPSM1	cis	parietal	SCAN
rs664026	SDCCAG3	cis	cerebellum	SCAN
rs664026	CELP	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136817000-136824400	Weak transcription	HepG2	liver
2	chr9:136821800-136828600	Enhancers	Primary B cells from cord blood	blood
3	chr9:136822400-136824600	Weak transcription	Brain Angular Gyrus	brain
4	chr9:136822400-136828800	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:136822600-136824200	Weak transcription	Fetal Heart	heart
6	chr9:136822600-136825000	Weak transcription	Fetal Brain Male	brain
7	chr9:136822600-136825400	Weak transcription	Fetal Intestine Large	intestine
8	chr9:136822600-136825600	Weak transcription	Brain Anterior Caudate	brain
9	chr9:136822600-136837000	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:136822800-136824200	Weak transcription	Liver	Liver
11	chr9:136822800-136824200	Weak transcription	Colonic Mucosa	Colon
12	chr9:136822800-136824400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:136822800-136824600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:136822800-136824800	Weak transcription	Brain Substantia Nigra	brain
15	chr9:136822800-136825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:136822800-136825800	Enhancers	Hela-S3	cervix
17	chr9:136822800-136828200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr9:136822800-136836600	Weak transcription	NHDF-Ad	bronchial
19	chr9:136823000-136824400	Weak transcription	Fetal Lung	lung
20	chr9:136823000-136825400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:136823000-136825400	Weak transcription	Left Ventricle	heart
22	chr9:136823000-136827600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr9:136823000-136829000	Weak transcription	Fetal Brain Female	brain
24	chr9:136823400-136824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:136823600-136824400	Enhancers	Placenta	Placenta
26	chr9:136823600-136824600	Enhancers	HUVEC	blood vessel
27	chr9:136823600-136824800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:136823600-136824800	Enhancers	HSMMtube	muscle
29	chr9:136823600-136825000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr9:136823600-136825000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:136823600-136825200	Enhancers	Fetal Thymus	thymus
32	chr9:136823600-136825400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:136823600-136825400	Enhancers	HMEC	breast
34	chr9:136823600-136825600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:136823600-136826200	Enhancers	HSMM	muscle
36	chr9:136823600-136826400	Enhancers	Fetal Muscle Trunk	muscle
37	chr9:136823600-136826800	Enhancers	Duodenum Mucosa	Duodenum
38	chr9:136823600-136827000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr9:136823600-136827000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:136823600-136827000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:136823600-136827200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr9:136823600-136827200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:136823600-136827200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:136823600-136827200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:136823600-136827200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr9:136823600-136827400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:136823600-136827400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:136823600-136827400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr9:136823600-136827400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr9:136823600-136827400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links