Variant report

Variant	rs311561
Chromosome Location	chr2:86291298-86291299
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86267588..86269329-chr2:86289160..86291639,2	K562	blood:

Variant related genes	Relation type
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10779967	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11885520	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12473739	1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13390107	1.00[ASN][1000 genomes]
rs13420958	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	1.00[ASN][1000 genomes]
rs1469982	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2059353	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288117	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311570	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311580	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311586	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34892520	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810828	1.00[ASN][1000 genomes]
rs4832027	1.00[ASN][1000 genomes]
rs4832028	0.91[ASN][1000 genomes]
rs4832239	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832254	1.00[ASN][1000 genomes]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6707736	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6715623	1.00[ASN][1000 genomes]
rs6720431	1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6749218	1.00[ASN][1000 genomes]
rs6752561	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847843	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	0.91[ASN][1000 genomes]
rs7558040	1.00[ASN][1000 genomes]
rs7583021	0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs889911	0.91[ASN][1000 genomes]
rs918856	1.00[ASN][1000 genomes]
rs929916	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679308	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs979940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs311561	POLR1A	cis	Nerve Tibial	GTEx
rs311561	MRPL35	cis	Esophagus Muscularis	GTEx
rs311561	MRPL35	cis	Artery Aorta	GTEx
rs311561	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:86268800-86295000	Strong transcription	Dnd41	blood
7	chr2:86280200-86293000	Weak transcription	Psoas Muscle	Psoas
8	chr2:86281400-86291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:86281400-86292400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:86282600-86299200	Weak transcription	Small Intestine	intestine
11	chr2:86282800-86291800	Weak transcription	Esophagus	oesophagus
12	chr2:86282800-86291800	Weak transcription	Gastric	stomach
13	chr2:86282800-86292000	Weak transcription	Spleen	Spleen
14	chr2:86282800-86295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:86283800-86291800	Weak transcription	Fetal Intestine Small	intestine
16	chr2:86284000-86292000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:86284200-86291400	Weak transcription	Thymus	Thymus
18	chr2:86285800-86294600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:86285800-86299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:86286000-86302200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:86286200-86292600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:86286200-86292600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:86286200-86292600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:86286200-86294200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:86286200-86298400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:86286200-86298600	Strong transcription	Fetal Lung	lung
29	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:86287000-86298800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:86287200-86294600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:86287400-86291800	Strong transcription	Fetal Brain Male	brain
34	chr2:86287400-86293000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:86287600-86293600	Strong transcription	Brain Hippocampus Middle	brain
36	chr2:86287600-86294000	Strong transcription	Primary T cells from cord blood	blood
37	chr2:86287600-86294000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:86287800-86293400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:86288400-86292000	Weak transcription	Pancreas	Pancrea
40	chr2:86288400-86294200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:86288600-86291800	Weak transcription	Fetal Stomach	stomach
42	chr2:86288800-86294200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:86289000-86291400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:86289000-86294400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:86289200-86291800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:86289200-86292000	Weak transcription	Aorta	Aorta
47	chr2:86289200-86292200	Weak transcription	Ovary	ovary
48	chr2:86289400-86291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:86289600-86292600	Weak transcription	HSMMtube	muscle
50	chr2:86289600-86293800	Strong transcription	HSMM	muscle

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