Variant report

Variant	rs34623781
Chromosome Location	chr12:9852445-9852446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9851988-9852621	H1-neurons	neurons:	n/a	n/a
2	MTA3	chr12:9852018-9852911	GM12878	blood:	n/a	n/a
3	NFIC	chr12:9852384-9852960	GM12878	blood:	n/a	chr12:9852809-9852825 chr12:9852809-9852826
4	POLR2A	chr12:9852000-9852653	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:9852312-9852472	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:9852027-9852658	GM12892	blood:	n/a	n/a
7	PML	chr12:9852166-9852458	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:9849159-9855177	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:9852147-9852573	GM12892	blood:	n/a	n/a
10	NFATC1	chr12:9852192-9852787	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:9852207-9853804	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:9852122-9852724	GM12878	blood:	n/a	n/a
13	REST	chr12:9851876-9853227	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr12:9852321-9855292	GM19193	blood:	n/a	n/a
15	POLR2A	chr12:9852160-9852576	GM12892	blood:	n/a	n/a
16	REST	chr12:9851969-9853374	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9851492..9853618-chr12:9859229..9860813,2	K562	blood:

Variant related genes	Relation type
ENSG00000256582	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10772060	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369995	0.89[ASN][1000 genomes]
rs12370579	0.89[ASN][1000 genomes]
rs12371503	0.89[ASN][1000 genomes]
rs12371981	0.89[ASN][1000 genomes]
rs12371982	0.89[ASN][1000 genomes]
rs12809752	0.89[ASN][1000 genomes]
rs12812783	0.89[ASN][1000 genomes]
rs12814560	0.89[ASN][1000 genomes]
rs12816660	0.89[ASN][1000 genomes]
rs12817550	0.89[ASN][1000 genomes]
rs12817743	0.89[ASN][1000 genomes]
rs12818179	0.89[ASN][1000 genomes]
rs12819865	0.89[ASN][1000 genomes]
rs12820674	0.89[ASN][1000 genomes]
rs12823653	0.89[ASN][1000 genomes]
rs12830448	0.89[ASN][1000 genomes]
rs12830867	0.89[ASN][1000 genomes]
rs12830878	0.89[ASN][1000 genomes]
rs1861089	0.89[ASN][1000 genomes]
rs2080207	0.89[ASN][1000 genomes]
rs34826829	0.89[ASN][1000 genomes]
rs35078787	0.89[ASN][1000 genomes]
rs35512621	0.89[ASN][1000 genomes]
rs4611290	0.88[AFR][1000 genomes]
rs4763280	0.89[ASN][1000 genomes]
rs4763814	0.89[ASN][1000 genomes]
rs4763819	0.89[ASN][1000 genomes]
rs66725265	0.89[ASN][1000 genomes]
rs67429242	0.89[ASN][1000 genomes]
rs71441764	0.89[ASN][1000 genomes]
rs7485402	0.89[ASN][1000 genomes]
rs7961812	0.89[ASN][1000 genomes]
rs7961903	0.89[ASN][1000 genomes]
rs7974554	0.89[ASN][1000 genomes]
rs7975557	0.89[ASN][1000 genomes]
rs7975865	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34623781	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs34623781	RP11-75L1.2	cis	Whole Blood	GTEx
rs34623781	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
2	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
4	chr12:9839000-9854400	Weak transcription	Lung	lung
5	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
6	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
8	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
9	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:9848400-9853000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:9848400-9854000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:9849400-9853000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:9849400-9853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:9849400-9854000	Weak transcription	Thymus	Thymus
19	chr12:9849800-9853200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:9849800-9854000	Weak transcription	Fetal Thymus	thymus
21	chr12:9849800-9860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:9850000-9854400	Weak transcription	Left Ventricle	heart
23	chr12:9850200-9854200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:9850400-9854400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:9850400-9854600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:9850800-9853400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:9851000-9853400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr12:9851200-9852800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:9851200-9854600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:9851400-9853200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:9851400-9853200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:9851400-9854400	Enhancers	Primary T cells from cord blood	blood
33	chr12:9851600-9852600	Weak transcription	Dnd41	blood
34	chr12:9851600-9852800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:9851600-9852800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:9851800-9852600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:9851800-9853600	Enhancers	HUVEC	blood vessel
38	chr12:9852000-9852800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:9852200-9852600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:9852200-9852600	Enhancers	Fetal Lung	lung
41	chr12:9852200-9852800	Enhancers	GM12878-XiMat	blood
42	chr12:9852200-9853000	Genic enhancers	Primary B cells from cord blood	blood
43	chr12:9852200-9854200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr12:9852200-9854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:9852200-9856400	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:9852400-9852600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:9852400-9852600	Enhancers	Colon Smooth Muscle	Colon
48	chr12:9852400-9852600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr12:9852400-9852600	Enhancers	Osteobl	bone
50	chr12:9852400-9852800	Flanking Active TSS	Fetal Heart	heart

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