Variant report

Variant	rs4671966
Chromosome Location	chr2:54899720-54899721
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54898899..54901777-chr2:54904985..54907433,2	K562	blood:
2	chr2:54891251..54894116-chr2:54898637..54900968,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1027950	0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1052788	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1052820	0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12475342	0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12475598	0.86[AFR][1000 genomes]
rs12611806	0.83[ASN][1000 genomes]
rs12612665	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12620195	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622340	0.86[ASN][1000 genomes]
rs1510612	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17045941	0.81[CEU][hapmap]
rs17046153	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17416284	0.80[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2007020	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs354188	0.80[ASN][1000 genomes]
rs354215	0.83[ASN][1000 genomes]
rs3796012	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3817163	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4283459	0.86[AFR][1000 genomes]
rs4671959	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4671962	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4671964	0.81[AMR][1000 genomes]
rs4671965	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4671968	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56898160	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59871921	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6545433	0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6545438	0.82[CHB][hapmap]
rs6705756	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6738725	0.80[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6739099	0.86[AFR][1000 genomes]
rs67457439	0.86[AFR][1000 genomes]
rs72618665	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72618666	0.82[EUR][1000 genomes]
rs72618667	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72618668	0.83[EUR][1000 genomes];0.86[ASN][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	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
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671966	EML6	cis	Artery Tibial	GTEx
rs4671966	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54891200-54899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54893800-54900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:54894600-54902200	Weak transcription	Psoas Muscle	Psoas
4	chr2:54894800-54900400	Weak transcription	Small Intestine	intestine
5	chr2:54894800-54900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:54895200-54900400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:54895400-54900200	Strong transcription	Fetal Muscle Leg	muscle
8	chr2:54895400-54900400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:54895800-54899800	Weak transcription	Right Atrium	heart
10	chr2:54895800-54900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:54895800-54900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:54895800-54902200	Weak transcription	Ovary	ovary
13	chr2:54896200-54899800	Weak transcription	Esophagus	oesophagus
14	chr2:54896800-54900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:54896800-54902400	Weak transcription	K562	blood
16	chr2:54897000-54900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:54897000-54900600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:54897000-54903800	Weak transcription	Brain Germinal Matrix	brain
19	chr2:54897200-54907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:54897400-54900600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:54897600-54899800	Weak transcription	Stomach Mucosa	stomach
22	chr2:54897600-54900000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:54897600-54900200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:54897600-54900400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:54897600-54902800	Weak transcription	Gastric	stomach
26	chr2:54897800-54899800	Weak transcription	Colonic Mucosa	Colon
27	chr2:54897800-54900200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:54897800-54901200	Strong transcription	A549	lung
29	chr2:54898000-54899800	Weak transcription	Left Ventricle	heart
30	chr2:54898000-54900400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:54898000-54901400	Weak transcription	Dnd41	blood
32	chr2:54898200-54899800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:54898200-54900000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:54898200-54900600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:54898200-54902600	Weak transcription	Fetal Heart	heart
36	chr2:54898200-54907000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:54898400-54899800	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:54898400-54900200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54898400-54900200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:54898400-54900400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:54898400-54900400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:54898400-54900400	Weak transcription	Fetal Stomach	stomach
43	chr2:54898400-54900600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:54898400-54900800	Weak transcription	Thymus	Thymus
45	chr2:54898400-54902800	Weak transcription	Aorta	Aorta
46	chr2:54898400-54904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:54898600-54899800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:54898600-54899800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:54898600-54899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:54898600-54899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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