Variant report

Variant	rs3185921
Chromosome Location	chr12:48734731-48734732
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	chr12:48733613..48735168-chr12:48738157..48739874,2	MCF-7	breast:
2	chr12:48591117..48593600-chr12:48733490..48736023,2	K562	blood:
3	chr12:48731724..48737573-chr12:48737990..48746470,14	K562	blood:
4	chr12:48732421..48734160-chr12:48734497..48737400,2	MCF-7	breast:
5	chr12:48732035..48733570-chr12:48734227..48737131,2	MCF-7	breast:
6	chr12:48729428..48731486-chr12:48731797..48736045,4	MCF-7	breast:
7	chr12:48731903..48736039-chr12:48740955..48745883,6	MCF-7	breast:
8	chr12:48718327..48723671-chr12:48729178..48735713,9	MCF-7	breast:
9	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000269514	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000187166	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1021313	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431526	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10437919	0.80[ASN][1000 genomes]
rs10437920	0.80[ASN][1000 genomes]
rs10467101	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs10875750	0.87[JPT][hapmap]
rs10875767	0.86[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.86[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs10875772	0.86[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs10875777	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875778	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875779	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875792	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875793	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875799	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168427	0.87[JPT][hapmap]
rs11168433	0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	0.86[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs11168487	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168493	0.83[ASN][1000 genomes]
rs11168508	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168510	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168514	0.87[ASN][1000 genomes]
rs11168516	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168520	0.95[ASN][1000 genomes]
rs11168536	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227601	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12297470	0.86[JPT][hapmap]
rs12305511	0.87[JPT][hapmap]
rs12310813	0.87[JPT][hapmap]
rs12312134	0.81[JPT][hapmap]
rs12313745	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12317751	0.80[ASN][1000 genomes]
rs12322347	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12322348	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122812	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054904	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279464	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450992	0.93[ASN][1000 genomes]
rs2634675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2732439	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2732465	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2898065	0.82[EUR][1000 genomes]
rs3751273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760622	0.87[JPT][hapmap]
rs4760625	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.87[JPT][hapmap]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs61941003	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61941006	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.85[JPT][hapmap]
rs716553	0.80[ASN][1000 genomes]
rs7297298	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303055	0.80[ASN][1000 genomes]
rs7486008	0.80[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs8804	0.87[JPT][hapmap]
rs9634261	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9788082	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1044444	chr12:48725007-48737570	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
11	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3185921	FAM186B	cis	parietal	SCAN
rs3185921	PFKM	cis	parietal	SCAN
rs3185921	IRAK4	cis	parietal	SCAN
rs3185921	RND1	cis	cerebellum	SCAN
rs3185921	H1FNT	cis	cerebellum	SCAN
rs3185921	TMEM106C	cis	cerebellum	SCAN
rs3185921	ZNF641	cis	cerebellum	SCAN
rs3185921	ZNF641	cis	Muscle Skeletal	GTEx
rs3185921	ASB8	cis	cerebellum	SCAN
rs3185921	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs3185921	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48723800-48736600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48724400-48736000	Weak transcription	Fetal Stomach	stomach
3	chr12:48725200-48735800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:48725200-48736800	Weak transcription	Hela-S3	cervix
5	chr12:48728000-48736000	Weak transcription	HSMMtube	muscle
6	chr12:48728600-48734800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:48728800-48736600	Weak transcription	Right Ventricle	heart
8	chr12:48728800-48737000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:48729000-48735600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:48729000-48735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:48729000-48736000	Weak transcription	Spleen	Spleen
12	chr12:48729000-48736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:48729000-48739200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:48729200-48736600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:48729200-48736600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:48729200-48736600	Weak transcription	Pancreas	Pancrea
17	chr12:48729200-48743400	Weak transcription	Stomach Mucosa	stomach
18	chr12:48729400-48736000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:48730000-48736000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:48730200-48736000	Weak transcription	Placenta	Placenta
21	chr12:48730200-48736600	Weak transcription	Ovary	ovary
22	chr12:48730400-48736400	Weak transcription	Lung	lung
23	chr12:48730600-48736800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:48730800-48736000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:48731000-48736000	Weak transcription	Fetal Lung	lung
26	chr12:48731000-48736400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:48731200-48738200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:48731200-48743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:48731400-48736200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:48731400-48736800	Weak transcription	Psoas Muscle	Psoas
31	chr12:48731600-48735400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:48731600-48735800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:48731600-48735800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:48731800-48736200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:48732000-48736600	Weak transcription	Gastric	stomach
36	chr12:48732000-48736600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:48732200-48735600	Weak transcription	Fetal Intestine Large	intestine
38	chr12:48732200-48736000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:48732400-48735200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:48732400-48735600	Weak transcription	Brain Germinal Matrix	brain
41	chr12:48732400-48735800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:48732400-48736800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:48732400-48742600	Strong transcription	Left Ventricle	heart
44	chr12:48732600-48735200	Strong transcription	Primary T cells from cord blood	blood
45	chr12:48732600-48736600	Weak transcription	Osteobl	bone
46	chr12:48732600-48736800	Weak transcription	GM12878-XiMat	blood
47	chr12:48732600-48738000	Weak transcription	Small Intestine	intestine
48	chr12:48732600-48742600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:48732800-48736000	Weak transcription	Brain Substantia Nigra	brain
50	chr12:48732800-48736600	Strong transcription	Primary T cells fromperipheralblood	blood

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