Variant report

Variant	rs6674929
Chromosome Location	chr1:153648661-153648662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153598471..153600111-chr1:153647680..153650652,2	K562	blood:
2	chr1:153543081..153545945-chr1:153646440..153648834,2	MCF-7	breast:
3	chr1:153648500..153651688-chr1:153746725..153749419,3	MCF-7	breast:
4	chr1:153648416..153650941-chr1:153651143..153653959,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169418	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10797056	0.88[JPT][hapmap]
rs10797096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908848	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265625	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265633	0.92[ASN][1000 genomes]
rs11548102	0.82[EUR][1000 genomes]
rs11588347	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139953	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12564925	0.88[JPT][hapmap]
rs12730186	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755890	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1888115	0.88[JPT][hapmap]
rs2274739	0.88[JPT][hapmap]
rs2274740	0.88[JPT][hapmap]
rs28380060	0.88[JPT][hapmap]
rs28518786	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28580554	0.88[JPT][hapmap]
rs28754733	0.88[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3790411	0.82[JPT][hapmap]
rs3790412	0.88[JPT][hapmap]
rs3795396	0.95[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs3806233	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs3806234	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3818632	0.88[JPT][hapmap]
rs3828031	0.88[JPT][hapmap]
rs3862047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4072425	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4310476	0.82[AMR][1000 genomes]
rs4351684	0.95[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4515830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4845563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845564	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55772653	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427640	0.84[ASN][1000 genomes]
rs66721814	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7345	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7934	0.88[JPT][hapmap]
rs913860	0.80[CHB][hapmap]
rs913861	0.88[JPT][hapmap]
rs9330298	0.84[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs9661993	0.91[ASN][1000 genomes]
rs9662664	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9700179	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs9700928	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs9726753	0.83[EUR][1000 genomes]
rs9792963	0.82[EUR][1000 genomes]
rs9792967	0.82[EUR][1000 genomes]

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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6674929	SCNM1	cis	parietal	SCAN
rs6674929	S100A13	cis	lymphoblastoid	seeQTL
rs6674929	S100A9	cis	parietal	SCAN
rs6674929	S100A4	cis	lymphoblastoid	seeQTL
rs6674929	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs6674929	S100A13	cis	parietal	SCAN
rs6674929	SLC27A3	cis	cerebellum	SCAN
rs6674929	S100A16	cis	cerebellum	SCAN
rs6674929	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs6674929	S100A16	cis	parietal	SCAN
rs6674929	S100A13	cis	multi-tissue	Pritchard
rs6674929	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs6674929	S100A2	cis	cerebellum	SCAN
rs6674929	S100A10	cis	cerebellum	SCAN
rs6674929	DCST2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153644600-153650400	Weak transcription	Esophagus	oesophagus
2	chr1:153645000-153649600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:153645000-153650000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:153645000-153650000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:153645000-153650000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:153645000-153650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:153645000-153650200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:153645200-153649200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:153645200-153650000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:153645600-153649800	Weak transcription	Hela-S3	cervix
11	chr1:153648600-153650400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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