Variant report

Variant	rs1424516
Chromosome Location	chr2:86395273-86395274
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	chr2:86394345..86397737-chr2:86420748..86423502,3	MCF-7	breast:
2	chr2:86393922..86396006-chr2:86396019..86398129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10187875	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10427394	0.87[CEU][hapmap]
rs10779967	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.88[MEX][hapmap]
rs11885520	0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	1.00[ASN][1000 genomes]
rs11891096	1.00[ASN][1000 genomes]
rs11895453	1.00[ASN][1000 genomes]
rs12473739	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13420958	1.00[ASN][1000 genomes]
rs1424520	0.87[CEU][hapmap]
rs1469982	1.00[ASN][1000 genomes]
rs1559513	1.00[JPT][hapmap]
rs1559516	0.87[CEU][hapmap]
rs2059353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288117	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288121	0.85[CEU][hapmap]
rs311561	1.00[ASN][1000 genomes]
rs311570	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs311580	1.00[ASN][1000 genomes]
rs311581	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs311582	1.00[ASN][1000 genomes]
rs311583	1.00[ASN][1000 genomes]
rs311584	1.00[ASN][1000 genomes]
rs34892520	0.92[ASN][1000 genomes]
rs3770073	0.84[ASN][1000 genomes]
rs3810828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832027	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs4832028	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832242	0.87[CEU][hapmap]
rs4832250	0.87[CEU][hapmap]
rs4832254	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4832258	1.00[JPT][hapmap]
rs58077381	1.00[ASN][1000 genomes]
rs6547666	1.00[JPT][hapmap]
rs6707736	0.84[ASN][1000 genomes]
rs6715623	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6758535	1.00[JPT][hapmap]
rs72847843	1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7558040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565645	1.00[JPT][hapmap]
rs7583021	0.82[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[ASN][1000 genomes]
rs889911	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs918856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929916	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	1.00[ASN][1000 genomes]
rs9679308	1.00[ASN][1000 genomes]
rs979940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
3	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1424516	POLR1A	cis	Nerve Tibial	GTEx
rs1424516	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs1424516	MRPL35	cis	Artery Aorta	GTEx
rs1424516	MRPL35	cis	Esophagus Muscularis	GTEx
rs1424516	POLR1A	cis	lymphoblastoid	seeQTL
rs1424516	C2orf23	cis	multi-tissue	Pritchard
rs1424516	MRPL35	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86335000-86409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86335400-86408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:86335600-86401000	Strong transcription	Placenta	Placenta
4	chr2:86335600-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:86335600-86408600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:86336000-86401200	Strong transcription	Adipose Nuclei	Adipose
7	chr2:86336800-86407400	Strong transcription	Dnd41	blood
8	chr2:86342000-86399800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:86342800-86408600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:86342800-86408600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:86343000-86408600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:86367600-86403400	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:86368000-86402000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:86368200-86400600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:86370600-86401400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:86371200-86398400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:86375200-86397000	Weak transcription	Small Intestine	intestine
18	chr2:86377600-86403200	Weak transcription	Stomach Mucosa	stomach
19	chr2:86378600-86401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:86379800-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:86380000-86400600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:86380000-86401400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:86381000-86400400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:86381000-86400800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:86381200-86401400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:86381600-86399600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:86381600-86400800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:86381600-86409000	Strong transcription	Fetal Thymus	thymus
29	chr2:86381800-86398600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:86381800-86399800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:86381800-86400000	Strong transcription	Left Ventricle	heart
32	chr2:86381800-86400200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:86381800-86401000	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:86381800-86401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:86381800-86401200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:86381800-86401400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:86381800-86401400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:86381800-86401600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:86381800-86401800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:86381800-86407400	Strong transcription	Liver	Liver
41	chr2:86381800-86409000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:86382000-86400000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:86382400-86399600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:86382600-86400400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:86383000-86398800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:86383600-86398200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:86384000-86400400	Strong transcription	Osteobl	bone
48	chr2:86384000-86400800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr2:86386200-86413000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:86387600-86410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links