Variant report

Variant	rs858513
Chromosome Location	chr7:99825558-99825559
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	chr7:99824985-99826539	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:99825427-99825955	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:99822111-99827275	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:99824869-99826521	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:99824867-99826370	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:99825381-99826397	GM12891	blood:	n/a	n/a
7	POLR2A	chr7:99822131-99826487	GM12892	blood:	n/a	n/a
8	POLR2A	chr7:99825428-99825591	Raji	blood:	n/a	n/a
9	POLR2A	chr7:99825388-99826397	GM12878	blood:	n/a	n/a
10	NFATC1	chr7:99825406-99825744	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:99825330-99826397	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:99824854-99826778	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239521	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10252884	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043915	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1052482	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953295	0.87[CHB][hapmap]
rs1138417	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11764176	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11767968	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666107	0.94[ASN][1000 genomes]
rs12666425	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705073	0.86[CHB][hapmap]
rs13230744	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1617502	0.82[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1618851	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1623264	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1624099	0.86[CHB][hapmap]
rs1628077	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1636975	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1636988	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1637001	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727122	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727123	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727124	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727125	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1727128	0.91[CHB][hapmap]
rs1727130	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727133	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727134	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727138	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727140	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727142	0.95[EUR][1000 genomes]
rs2005763	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141160	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246713	0.87[CHB][hapmap]
rs2257213	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272344	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272345	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405442	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2528900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906645	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906646	0.86[CHB][hapmap]
rs2950517	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950518	0.86[CHB][hapmap]
rs2950520	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34919929	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3735241	0.86[CHB][hapmap]
rs3735242	0.86[CHB][hapmap]
rs3779045	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3779046	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823642	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4729579	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55796551	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57966707	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6465764	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465765	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6948729	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6960458	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705867	0.86[CHB][hapmap]
rs7788301	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794170	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7811662	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs858507	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs858508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858509	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858514	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866500	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941287	0.86[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs858513	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs858513	GATS	cis	multi-tissue	Pritchard
rs858513	LOC389541	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

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	chr7:99811600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:99812400-99839600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:99813800-99829400	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:99813800-99838800	Weak transcription	Fetal Brain Male	brain
11	chr7:99813800-99841200	Weak transcription	Left Ventricle	heart
12	chr7:99813800-99846800	Weak transcription	Ovary	ovary
13	chr7:99815000-99828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr7:99815200-99828800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:99815400-99825600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:99815400-99834800	Weak transcription	A549	lung
17	chr7:99815400-99834800	Weak transcription	Osteobl	bone
18	chr7:99815600-99835200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:99815600-99844800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:99815800-99839600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:99816600-99826400	Strong transcription	Fetal Brain Female	brain
22	chr7:99816600-99827600	Weak transcription	Aorta	Aorta
23	chr7:99816800-99832000	Strong transcription	Fetal Intestine Small	intestine
24	chr7:99818000-99830400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:99818600-99826200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:99819400-99834800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:99819800-99829000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:99819800-99830800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:99819800-99832000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:99820200-99828600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:99820400-99828600	Weak transcription	Right Ventricle	heart
32	chr7:99820400-99834600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:99820800-99829000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:99820800-99835200	Weak transcription	HSMM	muscle
35	chr7:99821400-99828600	Weak transcription	Primary B cells from cord blood	blood
36	chr7:99821400-99828800	Weak transcription	Fetal Intestine Large	intestine
37	chr7:99821400-99831800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:99821400-99834800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:99821600-99828600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:99821600-99834800	Weak transcription	Brain Anterior Caudate	brain
41	chr7:99821600-99844000	Weak transcription	Esophagus	oesophagus
42	chr7:99821600-99867800	Weak transcription	Gastric	stomach
43	chr7:99821800-99828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:99821800-99834600	Weak transcription	Adipose Nuclei	Adipose
45	chr7:99821800-99839800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr7:99822000-99827000	Genic enhancers	Fetal Thymus	thymus
47	chr7:99822000-99828600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr7:99822000-99828600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:99822000-99828800	Weak transcription	Brain Substantia Nigra	brain
50	chr7:99822000-99834800	Weak transcription	Brain Angular Gyrus	brain

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