Variant report

Variant	rs2681779
Chromosome Location	chr3:50011021-50011022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49977360..49980004-chr3:50009456..50011405,3	K562	blood:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1061474	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs1062633	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10865959	0.86[CHB][hapmap]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs1138536	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs11709573	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11712056	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11714324	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11721204	0.81[ASN][1000 genomes]
rs12107768	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12496973	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13060128	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.85[ASN][1000 genomes]
rs13079006	0.81[ASN][1000 genomes]
rs13082703	0.88[ASN][1000 genomes]
rs1317140	0.89[CHB][hapmap]
rs17657664	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17657688	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1799843	0.89[CHB][hapmap]
rs1799845	0.89[CHB][hapmap]
rs2013208	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2230590	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240326	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240327	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240328	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap]
rs2240329	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2247510	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2252833	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2276864	0.86[CHB][hapmap]
rs2280406	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2352969	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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2352975	0.89[CHB][hapmap]
rs2352984	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2353579	0.82[JPT][hapmap]
rs2526747	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2526748	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526751	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526754	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2624821	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[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2624826	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs2624832	0.88[ASN][1000 genomes]
rs2624834	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2624843	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624847	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2624853	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.88[ASN][1000 genomes]
rs2681780	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681781	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2777888	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2856234	0.85[CHD][hapmap]
rs2856237	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2856238	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs2883057	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2883059	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs34034116	0.81[ASN][1000 genomes]
rs34312088	0.88[ASN][1000 genomes]
rs35275715	0.81[ASN][1000 genomes]
rs3733134	0.81[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3774759	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3796386	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4688688	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4688689	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4688755	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs62262114	0.84[ASN][1000 genomes]
rs6446193	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6762477	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6765484	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6792892	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6799579	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7061	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7430334	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7613875	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7621026	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7627864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7628058	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7629936	0.89[CHB][hapmap]
rs7648174	0.88[ASN][1000 genomes]
rs868891	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9311446	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs952594	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9814664	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9861216	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9866695	0.85[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2681779	RBM6	cis	parietal	SCAN
rs2681779	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs2681779	RBM6	cis	cerebellum	SCAN
rs2681779	C3orf18	cis	parietal	SCAN
rs2681779	C3orf78	cis	parietal	SCAN
rs2681779	CYB561D2	cis	cerebellum	SCAN
rs2681779	NCKIPSD	cis	parietal	SCAN
rs2681779	NCKIPSD	cis	cerebellum	SCAN
rs2681779	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
4	chr3:49997800-50013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
7	chr3:49998400-50078600	Weak transcription	K562	blood
8	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:49999800-50028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:50000000-50019600	Strong transcription	Dnd41	blood
11	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:50003800-50014600	Weak transcription	HSMMtube	muscle
14	chr3:50004200-50016000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:50004400-50027600	Weak transcription	NHEK	skin
16	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:50004800-50012600	Strong transcription	Fetal Intestine Small	intestine
18	chr3:50005000-50012600	Strong transcription	Fetal Stomach	stomach
19	chr3:50005000-50017400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:50005000-50027600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:50005000-50031400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:50005000-50036800	Weak transcription	Small Intestine	intestine
23	chr3:50005200-50033400	Weak transcription	Esophagus	oesophagus
24	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
25	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:50005400-50022000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:50005400-50022200	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:50005400-50036800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
30	chr3:50006200-50012600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:50006200-50014600	Weak transcription	Brain Substantia Nigra	brain
32	chr3:50006200-50027800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:50006200-50028200	Weak transcription	Right Ventricle	heart
34	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:50007000-50017600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:50007600-50020000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr3:50008200-50013800	Weak transcription	Hela-S3	cervix
38	chr3:50008400-50011800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:50008800-50016000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:50009000-50011600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:50009000-50011600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:50009000-50013200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:50009000-50013400	Strong transcription	Fetal Intestine Large	intestine
45	chr3:50009000-50013600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:50009000-50022800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:50009200-50011400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:50009200-50013000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:50009200-50013200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:50009200-50017800	Strong transcription	Fetal Thymus	thymus

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