Variant report

Variant	rs1623264
Chromosome Location	chr7:99811204-99811205
allele	C/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	chr7:99811114-99813826	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr7:99810553-99812339	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:99811112-99813917	GM12878	blood:	n/a	n/a
4	FOSL2	chr7:99810989-99812412	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:99811132-99811244	A549	lung:	n/a	n/a
6	POLR2A	chr7:99811135-99812096	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:99810825-99812775	HepG2	liver:	n/a	n/a
8	EBF1	chr7:99811131-99811767	GM12878	blood:	n/a	chr7:99811556-99811567 chr7:99811557-99811566 chr7:99811536-99811547

No.	Distal block	Cell Line	Cell type
1	chr7:99806182..99808834-chr7:99809702..99811286,2	MCF-7	breast:
2	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
3	chr7:99760958..99763450-chr7:99810400..99812602,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC2-2	chr7:99810646-99811247	NONHSAT122348

Variant related genes	Relation type
ENSG00000239521	TF binding region
PVRIG	TF binding region
ENSG00000066923	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10252884	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1043915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052482	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953295	0.87[CHB][hapmap]
rs1138417	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767968	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11771139	0.82[CEU][hapmap]
rs12666107	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12666425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705073	0.86[CHB][hapmap]
rs13230744	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1617502	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1618851	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624099	0.86[CHB][hapmap]
rs1628077	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1636975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1636988	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1637001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727122	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727123	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727124	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727125	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727128	0.91[CHB][hapmap];0.81[YRI][hapmap]
rs1727130	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727132	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1727142	0.97[EUR][1000 genomes]
rs1880949	0.83[CEU][hapmap]
rs2005763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141160	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246713	0.87[CHB][hapmap]
rs2257213	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272344	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272345	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405442	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2528900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906645	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906646	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs2950517	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2950518	0.86[CHB][hapmap]
rs2950520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35146811	0.83[CEU][hapmap]
rs3735241	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs3735242	0.86[CHB][hapmap]
rs3779045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779046	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823642	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4729579	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55796551	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57966707	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6465764	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6465765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465766	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6960458	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705867	0.86[CHB][hapmap]
rs7788301	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7794170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7811662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs858505	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858507	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs858508	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858509	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858511	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858512	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858513	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]
rs858514	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs863450	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs866500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941287	0.86[CHB][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv981557	chr7:99808038-99811640	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1623264	GATS	cis	multi-tissue	Pritchard
rs1623264	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
5	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
8	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:99803000-99816800	Weak transcription	Brain Angular Gyrus	brain
11	chr7:99803200-99813600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:99805200-99818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:99805600-99812800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr7:99806000-99812400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr7:99806800-99819000	Weak transcription	Fetal Lung	lung
16	chr7:99807200-99828400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:99807200-99847000	Weak transcription	Fetal Kidney	kidney
18	chr7:99807400-99815200	Weak transcription	Pancreas	Pancrea
19	chr7:99807600-99818400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:99807800-99812000	Weak transcription	K562	blood
21	chr7:99808000-99815200	Enhancers	Primary B cells from cord blood	blood
22	chr7:99808400-99813600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:99808800-99811600	Enhancers	Liver	Liver
24	chr7:99809000-99811400	Enhancers	HepG2	liver
25	chr7:99809000-99813400	Weak transcription	Brain Anterior Caudate	brain
26	chr7:99809000-99817600	Weak transcription	Small Intestine	intestine
27	chr7:99809200-99813000	Enhancers	Primary T cells from cord blood	blood
28	chr7:99809200-99817600	Weak transcription	Colonic Mucosa	Colon
29	chr7:99809200-99834800	Weak transcription	HSMMtube	muscle
30	chr7:99809400-99815000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr7:99809400-99817600	Weak transcription	Spleen	Spleen
32	chr7:99809400-99818200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:99809600-99812400	Enhancers	Fetal Intestine Small	intestine
34	chr7:99809600-99815000	Enhancers	Primary B cells from peripheral blood	blood
35	chr7:99809600-99815000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:99809600-99815200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:99809600-99816800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:99809600-99817600	Weak transcription	Dnd41	blood
39	chr7:99809600-99818600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:99809800-99811400	Enhancers	Fetal Intestine Large	intestine
41	chr7:99809800-99813800	Enhancers	Thymus	Thymus
42	chr7:99809800-99814400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:99809800-99815000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:99809800-99815000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:99809800-99815000	Enhancers	Fetal Thymus	thymus
46	chr7:99810000-99812000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:99810000-99813000	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:99810000-99813400	Weak transcription	Fetal Stomach	stomach
49	chr7:99810000-99813600	Enhancers	GM12878-XiMat	blood
50	chr7:99810000-99814400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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