Variant report

Variant	rs6743345
Chromosome Location	chr2:39443569-39443570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39441692..39443732-chr2:39444876..39447459,3	K562	blood:
2	chr2:39442096..39444486-chr2:39445586..39448502,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10175094	0.84[CHB][hapmap]
rs10175855	0.92[AMR][1000 genomes]
rs10185961	0.84[CHB][hapmap]
rs10194771	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10196407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10427162	0.80[AMR][1000 genomes]
rs10865146	0.90[MEX][hapmap];0.88[AMR][1000 genomes]
rs11124661	0.90[MEX][hapmap]
rs11124663	0.85[AMR][1000 genomes]
rs11124665	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124671	0.83[CHB][hapmap]
rs11124675	0.84[CHB][hapmap]
rs11673802	0.92[AMR][1000 genomes]
rs11677383	0.84[CHB][hapmap]
rs11677985	0.86[AMR][1000 genomes]
rs11689688	0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs12151392	0.84[CHB][hapmap]
rs12165133	0.83[AMR][1000 genomes]
rs12617901	0.92[CHB][hapmap]
rs12712631	0.89[AMR][1000 genomes]
rs12712633	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712634	0.84[CHB][hapmap];0.82[GIH][hapmap]
rs12712640	0.84[CHB][hapmap]
rs13031442	0.83[ASN][1000 genomes]
rs13425432	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1861733	0.81[CHB][hapmap]
rs1861734	0.84[CHB][hapmap];0.82[GIH][hapmap]
rs2024514	0.84[CHB][hapmap]
rs2136638	0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs3755171	0.84[CHB][hapmap]
rs3755176	0.84[CHB][hapmap]
rs3770664	0.92[CHB][hapmap]
rs3770671	0.84[CHB][hapmap];0.82[GIH][hapmap]
rs3770672	0.83[CHB][hapmap]
rs6544209	0.88[AMR][1000 genomes]
rs6544214	0.84[CHB][hapmap]
rs6709424	0.84[CHB][hapmap]
rs6714566	0.84[CHB][hapmap]
rs6761679	0.88[AMR][1000 genomes]
rs7340455	0.84[CHB][hapmap]
rs7573535	0.88[AMR][1000 genomes]
rs7573923	0.84[CHB][hapmap]
rs7584676	0.90[MEX][hapmap];0.88[AMR][1000 genomes]
rs7590889	0.88[AMR][1000 genomes]
rs9037	0.84[CHB][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers 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
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv1000658	chr2:39374206-39466374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6743345	KCNG3	cis	parietal	SCAN
rs6743345	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39411000-39448400	Weak transcription	HSMMtube	muscle
2	chr2:39419000-39455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:39423400-39470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39429800-39459600	Weak transcription	HSMM	muscle
5	chr2:39431600-39455000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:39431800-39455200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:39435400-39455600	Weak transcription	Left Ventricle	heart
8	chr2:39439400-39455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:39440400-39443600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:39441600-39443600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:39441800-39443600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:39441800-39443600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:39442000-39443600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:39442000-39443600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:39442600-39444000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:39442600-39455000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:39442800-39443600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:39442800-39443800	Enhancers	Primary T cells from cord blood	blood
19	chr2:39442800-39446000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:39442800-39447200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:39442800-39447600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:39443000-39443800	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:39443200-39443800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:39443200-39444000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:39443400-39443800	Enhancers	HepG2	liver
26	chr2:39443400-39444000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr2:39443400-39444400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:39443400-39444600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr2:39443400-39444600	Enhancers	Fetal Thymus	thymus
30	chr2:39443400-39444800	Flanking Active TSS	Dnd41	blood

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