Variant report

Variant	rs13230744
Chromosome Location	chr7:99797792-99797793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99796687..99799289-chr7:100025322..100027560,2	K562	blood:
2	chr7:99795781..99801540-chr7:99806649..99812120,7	K562	blood:
3	chr7:99797078..99799692-chr7:99801985..99803908,2	MCF-7	breast:
4	chr7:99744806..99747397-chr7:99797049..99799857,2	K562	blood:
5	chr7:99744806..99746598-chr7:99796497..99798549,2	K562	blood:

Variant related genes	Relation type
ENSG00000146834	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000188186	Chromatin interaction
ENSG00000239521	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10252884	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1043915	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1052482	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1061230	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1138417	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11764176	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11767968	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11771139	0.81[CEU][hapmap]
rs12666107	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12666425	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1617502	0.85[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1618851	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1623264	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1628077	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1636975	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1636988	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1637001	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727122	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1727123	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1727124	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1727125	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1727128	0.96[YRI][hapmap]
rs1727130	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727132	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727133	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727134	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727138	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727140	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727142	0.84[EUR][1000 genomes]
rs1727145	0.83[AFR][1000 genomes]
rs1880949	0.81[CEU][hapmap]
rs2005763	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2141160	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2257213	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2272344	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2272345	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2528900	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2906645	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2906646	0.96[YRI][hapmap]
rs2950517	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950520	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35146811	0.81[CEU][hapmap]
rs3735241	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs3779045	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3779046	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3823642	0.88[AMR][1000 genomes]
rs4299940	0.82[AFR][1000 genomes]
rs4729579	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55796551	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6465764	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6465765	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6465766	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6948729	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6960458	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7788301	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7794170	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs7811662	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs858505	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs858506	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs858507	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs858508	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs858509	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs858511	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs858512	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs858513	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs858514	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs863450	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs866500	1.00[CEU][hapmap]
rs941287	0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv5867	chr7:99766774-99799755	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13230744	GATS	cis	multi-tissue	Pritchard
rs13230744	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99775800-99798000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:99778600-99797800	Weak transcription	Fetal Intestine Small	intestine
3	chr7:99790000-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:99791400-99806800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:99793200-99797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:99793400-99798000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:99793400-99806000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:99793600-99805800	Weak transcription	Primary T cells from cord blood	blood
10	chr7:99794000-99798200	Weak transcription	Fetal Brain Female	brain
11	chr7:99794600-99797800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:99795000-99798800	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:99795400-99798800	Enhancers	Primary B cells from cord blood	blood
14	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:99795800-99798600	Enhancers	GM12878-XiMat	blood
16	chr7:99795800-99802400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:99795800-99807000	Weak transcription	Thymus	Thymus
18	chr7:99796000-99808400	Weak transcription	Brain Anterior Caudate	brain
19	chr7:99796200-99802200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:99796400-99798800	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:99796400-99808800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
23	chr7:99796800-99798600	Enhancers	Spleen	Spleen
24	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
25	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:99797000-99798200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:99797000-99798800	Genic enhancers	Fetal Thymus	thymus
28	chr7:99797200-99798000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:99797200-99798000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr7:99797200-99798400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr7:99797600-99798600	Flanking Active TSS	K562	blood

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