Variant report

Variant	rs4964794
Chromosome Location	chr12:104194418-104194419
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	chr12:104192629..104194904-chr12:104224915..104226874,2	MCF-7	breast:
2	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
3	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
4	chr12:104190724..104195360-chr12:104196501..104199658,6	MCF-7	breast:
5	chr12:104194168..104195687-chr12:104197418..104199673,2	K562	blood:
6	chr12:104190889..104195812-chr12:104232079..104236624,5	MCF-7	breast:
7	chr12:104192744..104195300-chr12:104227670..104230455,2	MCF-7	breast:
8	chr12:104192326..104196273-chr12:104235179..104237558,3	K562	blood:
9	chr12:104192025..104195229-chr12:104233820..104236988,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10861094	0.91[JPT][hapmap]
rs10861096	0.86[ASW][hapmap]
rs10861097	0.86[ASW][hapmap];0.82[MEX][hapmap]
rs10861099	0.86[ASW][hapmap];0.82[GIH][hapmap]
rs10861102	0.92[AFR][1000 genomes]
rs10861103	0.92[AFR][1000 genomes]
rs10861104	0.94[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10861105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861109	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11111772	0.90[AFR][1000 genomes]
rs11111773	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11111775	0.92[AFR][1000 genomes]
rs11111776	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11111779	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11111781	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11111782	1.00[ASW][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11111783	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11111786	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111787	0.90[AFR][1000 genomes]
rs11111788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111789	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111791	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11111792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111793	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111795	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111796	0.84[CEU][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12228207	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12229276	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12424737	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12830701	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370777	0.93[ASW][hapmap];0.82[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1370778	0.92[AFR][1000 genomes]
rs1370779	0.92[AFR][1000 genomes]
rs1866293	0.92[AFR][1000 genomes]
rs1866294	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1866295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1866296	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1968513	0.92[AFR][1000 genomes]
rs2888792	0.92[AFR][1000 genomes]
rs34307072	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35371470	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35746861	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35945096	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36034617	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751204	0.86[ASW][hapmap];0.82[MEX][hapmap]
rs3812803	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3935416	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964289	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964623	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964780	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964786	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4964805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4964813	0.92[AFR][1000 genomes]
rs4964814	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4964819	0.92[AFR][1000 genomes]
rs4964820	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs5001722	0.89[AFR][1000 genomes]
rs58421738	0.92[AFR][1000 genomes]
rs67825151	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7134701	0.86[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312606	0.92[AFR][1000 genomes]
rs7312825	0.92[AFR][1000 genomes]
rs73192049	0.87[AFR][1000 genomes]
rs73192053	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9132	0.86[ASW][hapmap];0.82[MEX][hapmap]
rs934843	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs934845	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs934846	0.92[AFR][1000 genomes]
rs934847	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs954921	0.86[ASW][hapmap]
rs9706225	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4964794	C12orf45	cis	cerebellum	SCAN
rs4964794	RP11-341G23.4	cis	Artery Tibial	GTEx
rs4964794	RP11-341G23.4	cis	Thyroid	GTEx
rs4964794	NT5DC3	cis	parietal	SCAN
rs4964794	SKA3	trans	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:104185800-104198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:104187800-104198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
11	chr12:104188600-104195600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:104188800-104195800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:104188800-104196400	Weak transcription	Thymus	Thymus
14	chr12:104190400-104196000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:104190800-104196000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:104190800-104198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:104190800-104201800	Weak transcription	Gastric	stomach
18	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:104191000-104195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:104191200-104195600	Weak transcription	Aorta	Aorta
23	chr12:104191800-104195600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:104192000-104194600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:104192000-104195000	Enhancers	Placenta	Placenta
26	chr12:104192000-104200400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:104192400-104195000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:104192800-104194600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:104192800-104195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:104192800-104195000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:104192800-104195000	Enhancers	Fetal Intestine Large	intestine
33	chr12:104192800-104196400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:104192800-104197000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:104192800-104199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:104193000-104194600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:104193000-104195200	Enhancers	Fetal Intestine Small	intestine
38	chr12:104193000-104196600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:104193000-104196800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:104193200-104194600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr12:104193200-104195000	Enhancers	Pancreas	Pancrea
43	chr12:104193200-104195000	Enhancers	Spleen	Spleen
44	chr12:104193200-104196200	Enhancers	Lung	lung
45	chr12:104193400-104194600	Enhancers	Right Atrium	heart
46	chr12:104193400-104194800	Enhancers	NHLF	lung
47	chr12:104193400-104195000	Enhancers	Fetal Lung	lung
48	chr12:104193400-104195000	Enhancers	Fetal Thymus	thymus
49	chr12:104193400-104195000	Flanking Active TSS	Hela-S3	cervix
50	chr12:104193400-104195200	Enhancers	Liver	Liver

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