Variant report

Variant	rs28521373
Chromosome Location	chr14:67738075-67738076
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	chr14:67737210..67739382-chr14:67748000..67750840,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71D-1	chr14:67736418-67738776	NONHSAT037435

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1006595	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10131984	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10132093	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10138850	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10138865	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10138952	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10141692	0.81[ASN][1000 genomes]
rs10141947	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10144122	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10145508	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10145511	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10147362	0.96[EUR][1000 genomes]
rs10149600	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10149615	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10150082	0.83[EUR][1000 genomes]
rs10150145	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1044745	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1073605	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11158653	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12588458	0.81[ASN][1000 genomes]
rs12590689	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12590956	0.81[ASN][1000 genomes]
rs1473732	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17104114	0.83[EUR][1000 genomes]
rs17104202	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17248252	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1918483	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2031564	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2039055	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2281676	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2296561	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2319777	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28718312	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784078	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3844530	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4636843	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57154550	0.81[ASN][1000 genomes]
rs59472119	0.81[ASN][1000 genomes]
rs59861720	0.80[ASN][1000 genomes]
rs60505324	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61612119	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6573747	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6573748	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6573752	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6573758	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6573760	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6573765	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573768	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7141519	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7147207	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7148044	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7148425	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7151898	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7156119	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7157394	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7157418	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7158228	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7161664	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73279056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73280987	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73282707	0.82[ASN][1000 genomes]
rs73284892	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7493580	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8003327	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8003929	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8004148	0.83[EUR][1000 genomes]
rs8004488	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8004798	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8005981	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8007696	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8008443	0.92[ASN][1000 genomes]
rs8009087	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8010261	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8015819	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8019510	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8021992	0.94[ASN][1000 genomes]
rs9323490	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9323491	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9323492	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9323493	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9743912	0.94[ASN][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	nsv902058	chr14:67310195-67760538	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv902059	chr14:67352226-67760538	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv902060	chr14:67417083-67760538	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv832821	chr14:67590418-67828169	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1040257	chr14:67634585-67762806	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS 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 miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28521373	EIF2S1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67709000-67740600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr14:67709800-67746000	Weak transcription	Primary B cells from cord blood	blood
3	chr14:67721400-67798400	Weak transcription	Hela-S3	cervix
4	chr14:67730800-67739200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:67730800-67769800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:67732400-67810000	Weak transcription	Gastric	stomach
7	chr14:67732600-67739000	Weak transcription	Dnd41	blood
8	chr14:67733600-67738600	Enhancers	Fetal Stomach	stomach
9	chr14:67733600-67747800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr14:67733800-67740600	Weak transcription	Spleen	Spleen
11	chr14:67734200-67760200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr14:67734800-67768600	Weak transcription	GM12878-XiMat	blood
13	chr14:67735000-67738400	Enhancers	Fetal Intestine Small	intestine
14	chr14:67735200-67760200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr14:67735400-67738400	Enhancers	Fetal Heart	heart
16	chr14:67735400-67745800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:67735400-67771600	Weak transcription	NHEK	skin
18	chr14:67735400-67778600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:67735400-67798400	Weak transcription	K562	blood
20	chr14:67735600-67738200	Enhancers	Colon Smooth Muscle	Colon
21	chr14:67735600-67738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr14:67735600-67739400	Weak transcription	Left Ventricle	heart
23	chr14:67735600-67751200	Weak transcription	Pancreas	Pancrea
24	chr14:67735600-67752800	Weak transcription	Esophagus	oesophagus
25	chr14:67735600-67754800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr14:67735600-67770000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr14:67735600-67772000	Weak transcription	Lung	lung
28	chr14:67735600-67810000	Weak transcription	Aorta	Aorta
29	chr14:67735800-67739000	Weak transcription	Small Intestine	intestine
30	chr14:67735800-67739200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr14:67735800-67739400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:67735800-67740400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr14:67736000-67738200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr14:67736000-67738200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr14:67736200-67742800	Weak transcription	HUVEC	blood vessel
36	chr14:67736200-67768600	Weak transcription	Fetal Thymus	thymus
37	chr14:67736400-67744000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr14:67736600-67738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr14:67736600-67738200	Genic enhancers	HSMM	muscle
40	chr14:67736600-67741800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr14:67736600-67762400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr14:67736600-67770600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:67736800-67738200	Enhancers	Brain Anterior Caudate	brain
44	chr14:67736800-67760400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr14:67737000-67738200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr14:67737000-67738200	Enhancers	Brain Hippocampus Middle	brain
47	chr14:67737000-67738200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr14:67737000-67738200	Enhancers	Fetal Kidney	kidney
49	chr14:67737000-67738200	Weak transcription	Right Atrium	heart
50	chr14:67737000-67738400	Enhancers	Cortex derived primary cultured neurospheres	brain

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