Variant report

Variant	rs4964805
Chromosome Location	chr12:104192824-104192825
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr12:104187183..104188924-chr12:104191126..104192831,2	K562	blood:
4	chr12:104190724..104195360-chr12:104196501..104199658,6	MCF-7	breast:
5	chr12:104190889..104195812-chr12:104232079..104236624,5	MCF-7	breast:
6	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
7	chr12:104192165..104193945-chr12:104199242..104201108,2	K562	blood:
8	chr12:104192744..104195300-chr12:104227670..104230455,2	MCF-7	breast:
9	chr12:104192326..104196273-chr12:104235179..104237558,3	K562	blood:
10	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: 83 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10861094	0.80[CHB][hapmap];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	0.95[AFR][1000 genomes]
rs10861103	0.95[AFR][1000 genomes]
rs10861104	0.94[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861105	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861109	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111772	0.92[AFR][1000 genomes]
rs11111773	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11111775	0.95[AFR][1000 genomes]
rs11111776	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11111779	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111781	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11111782	1.00[ASW][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11111783	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs11111786	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11111787	0.92[AFR][1000 genomes]
rs11111788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11111789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11111791	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111792	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11111793	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11111795	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111796	0.84[CEU][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12228207	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12229276	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12424737	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12830701	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	0.95[AFR][1000 genomes]
rs1370779	0.95[AFR][1000 genomes]
rs1866293	0.95[AFR][1000 genomes]
rs1866294	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1866295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1866296	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1968513	0.95[AFR][1000 genomes]
rs2888792	0.95[AFR][1000 genomes]
rs34307072	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35371470	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35746861	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35945096	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36034617	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751204	0.86[ASW][hapmap];0.82[MEX][hapmap]
rs3812803	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935416	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964289	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4964623	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964780	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4964786	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4964794	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];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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964812	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4964813	0.95[AFR][1000 genomes]
rs4964814	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4964819	0.95[AFR][1000 genomes]
rs4964820	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs5001722	0.91[AFR][1000 genomes]
rs58421738	0.95[AFR][1000 genomes]
rs67825151	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7134701	0.86[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312606	0.95[AFR][1000 genomes]
rs7312825	0.95[AFR][1000 genomes]
rs73192049	0.89[AFR][1000 genomes]
rs73192053	0.86[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];0.95[AFR][1000 genomes]
rs934845	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs934846	0.95[AFR][1000 genomes]
rs934847	0.93[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs954921	0.86[ASW][hapmap]
rs9706225	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv52873	chr12:104191266-104193582	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Attention deficit hyperactivity disorder	18839057	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4964805	RP11-341G23.4	cis	Thyroid	GTEx
rs4964805	RP11-341G23.4	cis	Artery Tibial	GTEx
rs4964805	TU12B1-TY	cis	multi-tissue	Pritchard
rs4964805	C12orf45	cis	cerebellum	SCAN
rs4964805	NT5DC3	cis	parietal	SCAN
rs4964805	SKA3	trans	parietal	SCAN

Chromatin state (count:118 , 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	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
3	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
12	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
13	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
14	chr12:104179000-104193200	Weak transcription	Spleen	Spleen
15	chr12:104179000-104193600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:104179400-104193800	Weak transcription	Fetal Kidney	kidney
17	chr12:104179800-104193800	Weak transcription	NHDF-Ad	bronchial
18	chr12:104183800-104193600	Weak transcription	Stomach Mucosa	stomach
19	chr12:104184800-104193400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:104185400-104193600	Strong transcription	Primary T cells from cord blood	blood
21	chr12:104185400-104193800	Strong transcription	K562	blood
22	chr12:104185800-104198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:104186600-104194400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:104187600-104193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:104187600-104193200	Weak transcription	Pancreas	Pancrea
27	chr12:104187600-104193600	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:104187600-104193600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:104187800-104193600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:104187800-104193800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:104187800-104198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
33	chr12:104188200-104193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:104188600-104193000	Strong transcription	HepG2	liver
35	chr12:104188600-104195600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:104188800-104193200	Weak transcription	Colonic Mucosa	Colon
37	chr12:104188800-104193200	Weak transcription	Lung	lung
38	chr12:104188800-104193400	Weak transcription	Fetal Thymus	thymus
39	chr12:104188800-104195800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:104188800-104196400	Weak transcription	Thymus	Thymus
41	chr12:104189000-104193200	Weak transcription	Brain Germinal Matrix	brain
42	chr12:104189000-104193600	Weak transcription	Brain Anterior Caudate	brain
43	chr12:104189000-104193600	Weak transcription	HSMMtube	muscle
44	chr12:104189200-104193600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:104189200-104193600	Weak transcription	Fetal Heart	heart
46	chr12:104189200-104193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:104189200-104194000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:104189200-104194000	Weak transcription	Fetal Brain Male	brain
49	chr12:104189200-104194200	Weak transcription	Fetal Brain Female	brain
50	chr12:104189200-104194200	Weak transcription	Right Ventricle	heart

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