Variant report

Variant	rs10187547
Chromosome Location	chr2:86312274-86312275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86309842..86313098-chr2:86314384..86317204,4	K562	blood:
2	chr2:86311786..86314563-chr2:86320003..86323114,3	K562	blood:
3	chr2:86307989..86312463-chr2:86330808..86334820,6	MCF-7	breast:
4	chr2:86311541..86313169-chr2:86331397..86334036,2	MCF-7	breast:
5	chr2:86309970..86313098-chr2:86314299..86317204,4	K562	blood:

Variant related genes	Relation type
ENSG00000132300	Chromatin interaction
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10176454	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10183744	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1019592	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1025104	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1075622	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11127012	0.86[ASN][1000 genomes]
rs11679343	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11686963	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694973	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12053229	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12714168	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1424517	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1559515	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1559517	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1834163	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991106	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2241436	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278086	0.80[ASN][1000 genomes]
rs2288118	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288119	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288120	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2367201	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2367202	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3088038	0.88[ASN][1000 genomes]
rs311563	0.89[ASN][1000 genomes]
rs311565	0.89[ASN][1000 genomes]
rs311569	0.89[ASN][1000 genomes]
rs311571	0.89[ASN][1000 genomes]
rs311572	0.88[ASN][1000 genomes]
rs311573	0.89[ASN][1000 genomes]
rs311587	0.85[ASN][1000 genomes]
rs3731820	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770069	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4618054	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832021	0.89[ASN][1000 genomes]
rs4832022	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832241	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4832245	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832246	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832247	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832248	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832249	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832251	0.88[ASN][1000 genomes]
rs59947468	0.82[ASN][1000 genomes]
rs60479377	0.82[ASN][1000 genomes]
rs60719866	0.82[ASN][1000 genomes]
rs61620607	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720327	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6740228	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6741577	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750581	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759862	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs725046	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559420	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7598787	0.88[ASN][1000 genomes]
rs7606421	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
14	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
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10187547	POLR1A	cis	Nerve Tibial	GTEx
rs10187547	POLR1A	cis	lung	GTEx
rs10187547	POLR1A	cis	Thyroid	GTEx
rs10187547	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs10187547	POLR1A	cis	Artery Tibial	GTEx
rs10187547	POLR1A	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 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	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86290800-86314600	Strong transcription	HMEC	breast
7	chr2:86290800-86318600	Strong transcription	K562	blood
8	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:86295200-86323200	Strong transcription	Fetal Stomach	stomach
13	chr2:86296000-86322400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:86300000-86318200	Strong transcription	Placenta	Placenta
15	chr2:86300000-86323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:86300000-86331800	Weak transcription	Stomach Mucosa	stomach
17	chr2:86301200-86318200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:86304600-86322400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:86304800-86313400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:86305400-86312400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:86306200-86327600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:86307600-86312800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:86307800-86322000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:86307800-86327600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:86307800-86331000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:86308000-86313000	Weak transcription	Psoas Muscle	Psoas
27	chr2:86308000-86313400	Weak transcription	Fetal Kidney	kidney
28	chr2:86308000-86315600	Weak transcription	Colonic Mucosa	Colon
29	chr2:86308000-86319800	Strong transcription	Primary T cells from cord blood	blood
30	chr2:86308000-86320800	Weak transcription	Fetal Brain Male	brain
31	chr2:86308000-86328400	Strong transcription	Dnd41	blood
32	chr2:86308000-86330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:86308200-86312400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:86308200-86312400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:86308200-86312400	Weak transcription	Gastric	stomach
36	chr2:86308200-86312400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:86308200-86312600	Weak transcription	Hela-S3	cervix
38	chr2:86308200-86312600	Weak transcription	HSMMtube	muscle
39	chr2:86308200-86313400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:86308200-86313400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:86308200-86313400	Weak transcription	NHLF	lung
42	chr2:86308200-86313600	Weak transcription	Primary B cells from cord blood	blood
43	chr2:86308200-86313600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:86308200-86313600	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:86308200-86313600	Weak transcription	NHDF-Ad	bronchial
46	chr2:86308200-86315400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:86308200-86315400	Weak transcription	Small Intestine	intestine
48	chr2:86308200-86316000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:86308200-86316200	Weak transcription	HUVEC	blood vessel
50	chr2:86308200-86322200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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