Variant report

Variant	rs3779045
Chromosome Location	chr7:99779259-99779260
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	SPI1	chr7:99779142-99779306	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99754637..99756174-chr7:99779153..99781591,2	MCF-7	breast:

Variant related genes	Relation type
GPC2	TF binding region
ENSG00000146826	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10252884	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052482	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953295	0.87[CHB][hapmap]
rs1138417	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11764176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11767968	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11771139	0.83[CEU][hapmap]
rs12666107	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12666425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12705073	0.86[CHB][hapmap]
rs13230744	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1617502	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1618851	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623264	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]
rs1624099	0.86[CHB][hapmap]
rs1628077	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1636975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1636988	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1637001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727122	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1727123	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727124	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727125	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1727128	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs1727130	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727132	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1727138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1727140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1727142	0.92[EUR][1000 genomes]
rs1880949	0.83[CEU][hapmap]
rs2005763	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2141160	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246713	0.87[CHB][hapmap]
rs2257213	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272344	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272345	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2405442	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2528900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906645	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2906646	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs2950517	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2950518	0.86[CHB][hapmap]
rs2950520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35146811	0.83[CEU][hapmap]
rs3735241	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs3735242	0.86[CHB][hapmap]
rs3779046	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823642	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4729579	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55796551	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57966707	0.80[EUR][1000 genomes]
rs6465764	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465765	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465766	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6948729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960458	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705867	0.86[CHB][hapmap]
rs7788301	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7811662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858505	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs858507	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs858508	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858509	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858511	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858512	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858513	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858514	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs863450	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs866500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs941287	0.86[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv966866	chr7:99778337-99792754	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3779045	GATS	cis	multi-tissue	Pritchard
rs3779045	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99775000-99780600	Enhancers	Primary T cells from cord blood	blood
2	chr7:99775800-99779400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr7:99775800-99787600	Weak transcription	GM12878-XiMat	blood
4	chr7:99775800-99798000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:99776000-99780400	Enhancers	Fetal Thymus	thymus
6	chr7:99777800-99779400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr7:99777800-99779600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:99778000-99779400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:99778000-99779400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:99778200-99779800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:99778400-99779400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:99778400-99779600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr7:99778600-99797800	Weak transcription	Fetal Intestine Small	intestine
14	chr7:99778800-99779400	Enhancers	Dnd41	blood
15	chr7:99778800-99780600	Enhancers	K562	blood
16	chr7:99778800-99787400	Weak transcription	Thymus	Thymus
17	chr7:99779000-99780200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:99779000-99780400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr7:99779000-99787400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:99779200-99779400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:99779200-99779600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:99779200-99779800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr7:99779200-99779800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:99779200-99779800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr7:99779200-99780400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:99779200-99787800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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