Variant report

Variant	rs3796014
Chromosome Location	chr2:54839276-54839277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
2	chr2:54829846..54832829-chr2:54836570..54839601,3	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10165490	1.00[YRI][hapmap]
rs10180713	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11885703	0.83[EUR][1000 genomes]
rs11892788	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11898012	0.86[TSI][hapmap];1.00[YRI][hapmap]
rs12104998	0.86[CEU][hapmap];0.88[GIH][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs12105792	1.00[ASW][hapmap];0.86[CEU][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12468469	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12617036	0.85[EUR][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13399435	1.00[YRI][hapmap]
rs1367295	0.86[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1510611	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1541854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs168506	0.81[EUR][1000 genomes]
rs171350	0.83[EUR][1000 genomes]
rs17344072	0.82[CEU][hapmap];0.80[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs17521078	0.86[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1864493	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2048371	0.83[EUR][1000 genomes]
rs2271322	0.85[EUR][1000 genomes]
rs2292356	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292357	0.91[EUR][1000 genomes]
rs2931463	0.86[EUR][1000 genomes]
rs2931464	0.86[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2941586	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2941587	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2941591	0.86[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971875	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3106204	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs354213	0.84[EUR][1000 genomes]
rs354226	0.81[EUR][1000 genomes]
rs354228	0.84[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs354236	0.84[TSI][hapmap]
rs4233952	0.81[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4455199	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4592889	0.87[EUR][1000 genomes]
rs4671221	0.81[CEU][hapmap];0.83[GIH][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4671222	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671225	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4671226	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671945	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671946	0.85[EUR][1000 genomes]
rs4671947	0.85[EUR][1000 genomes]
rs4671949	0.87[EUR][1000 genomes]
rs4671950	0.83[TSI][hapmap]
rs4671951	1.00[ASW][hapmap];0.82[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4671955	0.83[EUR][1000 genomes]
rs4671956	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671960	0.83[TSI][hapmap]
rs4671961	0.84[TSI][hapmap]
rs4990319	0.85[EUR][1000 genomes]
rs6545411	0.91[TSI][hapmap]
rs6545415	0.88[TSI][hapmap]
rs6545418	0.82[EUR][1000 genomes]
rs6545419	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6545427	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6545434	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704769	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6706372	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6724590	0.82[EUR][1000 genomes]
rs6729826	0.82[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6731661	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6732949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6734658	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6735813	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6746016	1.00[YRI][hapmap]
rs6746306	0.82[EUR][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6760298	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6761369	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6761398	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7563706	0.82[EUR][1000 genomes]
rs7589236	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7607451	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs907135	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796014	EML6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54832200-54840800	Weak transcription	K562	blood
3	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54832800-54839600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr2:54833000-54839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:54833000-54839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:54833000-54839400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:54833000-54839600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:54833000-54841000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
12	chr2:54833600-54839600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:54833600-54840000	Weak transcription	Fetal Kidney	kidney
14	chr2:54833800-54840800	Weak transcription	HMEC	breast
15	chr2:54834000-54839400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:54834200-54839400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:54835400-54842600	Enhancers	Fetal Heart	heart
18	chr2:54835800-54839400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:54836200-54842600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:54836800-54839600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:54836800-54841400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:54837000-54840200	Weak transcription	Aorta	Aorta
23	chr2:54837200-54839400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:54837400-54841600	Genic enhancers	HepG2	liver
25	chr2:54837400-54842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:54837800-54842600	Weak transcription	Small Intestine	intestine
27	chr2:54838000-54839400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:54838000-54839400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:54838000-54839600	Weak transcription	Stomach Mucosa	stomach
30	chr2:54838200-54839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:54838200-54839400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:54838200-54839400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:54838200-54839400	Weak transcription	Brain Angular Gyrus	brain
34	chr2:54838200-54839400	Weak transcription	NHDF-Ad	bronchial
35	chr2:54838200-54840800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:54838200-54842600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:54838200-54842800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:54838200-54843400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr2:54838600-54840000	Genic enhancers	A549	lung
40	chr2:54838600-54845600	Strong transcription	GM12878-XiMat	blood
41	chr2:54838800-54839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:54838800-54839400	Strong transcription	NH-A	brain
43	chr2:54838800-54840000	Strong transcription	Osteobl	bone
44	chr2:54838800-54841000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:54838800-54841200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:54838800-54843800	Genic enhancers	Brain Hippocampus Middle	brain
47	chr2:54838800-54845800	Strong transcription	Primary B cells from cord blood	blood
48	chr2:54838800-54845800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:54838800-54846200	Enhancers	Right Atrium	heart
50	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links