Variant report

Variant	rs35642909
Chromosome Location	chr12:9806405-9806406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
3	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:

Variant related genes	Relation type
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10466762	1.00[ASN][1000 genomes]
rs10772005	1.00[ASN][1000 genomes]
rs10772006	1.00[ASN][1000 genomes]
rs10844236	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844267	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10844327	1.00[ASN][1000 genomes]
rs10844350	1.00[ASN][1000 genomes]
rs10844351	1.00[ASN][1000 genomes]
rs10844352	1.00[ASN][1000 genomes]
rs10844353	1.00[ASN][1000 genomes]
rs10844359	1.00[ASN][1000 genomes]
rs10844369	0.89[ASN][1000 genomes]
rs11052207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052235	1.00[ASN][1000 genomes]
rs11052245	1.00[ASN][1000 genomes]
rs11052254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11608817	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310789	1.00[ASN][1000 genomes]
rs12366653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366792	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12809846	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12820641	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12830419	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12831287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560008	1.00[ASN][1000 genomes]
rs16913477	1.00[ASN][1000 genomes]
rs1863871	1.00[ASN][1000 genomes]
rs2114869	1.00[ASN][1000 genomes]
rs2162657	1.00[ASN][1000 genomes]
rs34323946	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34833649	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34981673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015427	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35098654	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35181877	0.89[ASN][1000 genomes]
rs35280686	1.00[ASN][1000 genomes]
rs35561167	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35671537	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35884213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55873283	1.00[ASN][1000 genomes]
rs61916061	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488065	0.89[ASN][1000 genomes]
rs7132037	1.00[ASN][1000 genomes]
rs7136821	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299738	1.00[ASN][1000 genomes]
rs7302110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302746	1.00[ASN][1000 genomes]
rs7303246	0.89[ASN][1000 genomes]
rs7304321	1.00[ASN][1000 genomes]
rs7304464	1.00[ASN][1000 genomes]
rs7305937	1.00[ASN][1000 genomes]
rs7309800	1.00[ASN][1000 genomes]
rs7310405	1.00[ASN][1000 genomes]
rs7310516	1.00[ASN][1000 genomes]
rs7310568	1.00[ASN][1000 genomes]
rs7310790	1.00[ASN][1000 genomes]
rs7311421	1.00[ASN][1000 genomes]
rs7311574	1.00[ASN][1000 genomes]
rs7311945	1.00[ASN][1000 genomes]
rs7959406	1.00[ASN][1000 genomes]
rs7959726	1.00[ASN][1000 genomes]
rs7961262	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962321	1.00[ASN][1000 genomes]
rs7967102	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973603	1.00[ASN][1000 genomes]
rs7974871	1.00[ASN][1000 genomes]
rs7978187	1.00[ASN][1000 genomes]
rs958340	1.00[ASN][1000 genomes]
rs9919786	1.00[ASN][1000 genomes]
rs9919787	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35642909	RP11-705C15.3	cis	Skin Sun Exposed Lower leg	GTEx
rs35642909	CLEC2D	cis	Thyroid	GTEx
rs35642909	RP11-705C15.3	cis	Whole Blood	GTEx
rs35642909	CLEC2D	cis	Esophagus Muscularis	GTEx
rs35642909	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9811200	Weak transcription	Gastric	stomach
2	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9802200-9806600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
6	chr12:9802600-9807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:9802600-9812800	Weak transcription	Ovary	ovary
8	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:9803000-9806600	Weak transcription	Placenta	Placenta
10	chr12:9803000-9806600	Weak transcription	Psoas Muscle	Psoas
11	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
14	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
16	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
17	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
18	chr12:9803200-9812400	Weak transcription	Liver	Liver
19	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:9803600-9806600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:9803600-9806800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
24	chr12:9803800-9806600	Weak transcription	Adipose Nuclei	Adipose
25	chr12:9804000-9806800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:9804000-9806800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:9804200-9806600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:9804200-9806600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:9804200-9806600	Weak transcription	HSMMtube	muscle
31	chr12:9804200-9807800	Weak transcription	Aorta	Aorta
32	chr12:9804200-9811200	Weak transcription	Right Ventricle	heart
33	chr12:9804200-9812400	Weak transcription	Brain Anterior Caudate	brain
34	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
36	chr12:9804200-9814600	Weak transcription	Lung	lung
37	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:9804400-9806600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:9804400-9806600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:9804400-9806600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:9804400-9806600	Weak transcription	Fetal Lung	lung
42	chr12:9804400-9806600	Weak transcription	Left Ventricle	heart
43	chr12:9804400-9806600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:9804400-9806800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:9804400-9806800	Weak transcription	NHLF	lung
46	chr12:9804400-9807000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:9804400-9807000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:9804400-9807000	Weak transcription	Hela-S3	cervix
49	chr12:9804400-9809400	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:9804400-9810800	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links