Variant report

Variant	rs858511
Chromosome Location	chr7:99823621-99823622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99823580-99824754	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:99822111-99827275	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:99821988-99824849	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:99823390-99823625	GM12878	blood:	n/a	n/a
5	MTA3	chr7:99823507-99824354	GM12878	blood:	n/a	n/a
6	PML	chr7:99823564-99824020	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:99822131-99826487	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:99823480-99824826	GM12891	blood:	n/a	n/a
9	POLR2A	chr7:99823482-99824780	GM12891	blood:	n/a	n/a
10	POLR2A	chr7:99823516-99824632	GM12891	blood:	n/a	n/a
11	POLR2A	chr7:99816181-99824845	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:99822306-99824757	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:99822259-99824853	GM12891	blood:	n/a	n/a
14	POLR2A	chr7:99823570-99823830	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239521	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10252884	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1043915	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052482	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061230	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1138417	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11764176	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11767968	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12666107	0.90[ASN][1000 genomes]
rs12666425	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13230744	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1617502	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1618851	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1623264	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1628077	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1636975	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1636988	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1637001	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727122	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727123	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727124	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727125	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727130	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727133	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727134	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727138	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727140	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727142	0.95[EUR][1000 genomes]
rs2005763	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141160	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2257213	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272344	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272345	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2528900	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2906645	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950517	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2950520	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779045	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3779046	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3823642	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4729579	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55796551	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57966707	0.81[EUR][1000 genomes]
rs6465764	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6465765	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6948729	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960458	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7788301	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7811662	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858506	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858507	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858509	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858514	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs866500	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
3	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS 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	51 gene(s)	inside rSNPs	diseases
6	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv888774	chr7:99807265-99951315	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	esv16057	chr7:99809377-99937347	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv3379367	chr7:99811760-99938687	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv3379649	chr7:99812207-99939196	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
13	esv3358931	chr7:99816130-99943645	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	esv3405423	chr7:99816156-99943860	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	esv3508070	chr7:99816206-99943813	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	esv3508071	chr7:99816206-99943813	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
17	nsv970560	chr7:99821528-99832022	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs858511	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs858511	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:99807200-99828400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:99807200-99847000	Weak transcription	Fetal Kidney	kidney
4	chr7:99809200-99834800	Weak transcription	HSMMtube	muscle
5	chr7:99810600-99864000	Weak transcription	Right Atrium	heart
6	chr7:99811400-99828600	Weak transcription	HepG2	liver
7	chr7:99811600-99823800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:99811600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:99812200-99823800	Weak transcription	Stomach Mucosa	stomach
10	chr7:99812400-99839600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:99813800-99825000	Weak transcription	Psoas Muscle	Psoas
12	chr7:99813800-99829400	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:99813800-99838800	Weak transcription	Fetal Brain Male	brain
14	chr7:99813800-99841200	Weak transcription	Left Ventricle	heart
15	chr7:99813800-99846800	Weak transcription	Ovary	ovary
16	chr7:99815000-99828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:99815200-99828800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:99815400-99825600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:99815400-99834800	Weak transcription	A549	lung
20	chr7:99815400-99834800	Weak transcription	Osteobl	bone
21	chr7:99815600-99835200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr7:99815600-99844800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:99815800-99839600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:99816600-99826400	Strong transcription	Fetal Brain Female	brain
25	chr7:99816600-99827600	Weak transcription	Aorta	Aorta
26	chr7:99816800-99824800	Strong transcription	Brain Germinal Matrix	brain
27	chr7:99816800-99825200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr7:99816800-99832000	Strong transcription	Fetal Intestine Small	intestine
29	chr7:99817000-99824200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:99817000-99824200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr7:99818000-99830400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:99818600-99824600	Strong transcription	Fetal Muscle Leg	muscle
33	chr7:99818600-99826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:99818800-99823800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:99819000-99824000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:99819400-99834800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:99819600-99824000	Weak transcription	Colonic Mucosa	Colon
38	chr7:99819800-99829000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:99819800-99830800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:99819800-99832000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:99820000-99824000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr7:99820000-99824200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:99820000-99825400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr7:99820200-99828600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:99820400-99823800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr7:99820400-99824400	Strong transcription	Dnd41	blood
47	chr7:99820400-99828600	Weak transcription	Right Ventricle	heart
48	chr7:99820400-99834600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:99820600-99824000	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr7:99820800-99829000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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