Variant report

Variant	rs617135
Chromosome Location	chr11:59936757-59936758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:59929729..59931318-chr11:59936371..59938548,3	K562	blood:
2	chr11:59936023..59937006-chr11:59960779..59961684,2	MCF-7	breast:
3	chr11:59926973..59929170-chr11:59934444..59937067,2	K562	blood:

Variant related genes	Relation type
ENSG00000254952	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs107903	0.89[JPT][hapmap]
rs1303615	0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap]
rs1303621	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs1441586	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs476722	0.89[JPT][hapmap]
rs502419	0.89[JPT][hapmap]
rs502581	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs516478	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs521952	0.89[JPT][hapmap]
rs525794	0.90[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs540170	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs556917	0.89[JPT][hapmap]
rs56189574	0.88[EUR][1000 genomes]
rs569046	0.86[JPT][hapmap]
rs574695	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs574704	0.89[JPT][hapmap]
rs581133	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs583296	0.90[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs583791	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs602396	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs606588	0.86[JPT][hapmap]
rs610932	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617916	0.88[JPT][hapmap]
rs624663	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631853	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs632185	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634475	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636147	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs652354	0.81[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs662196	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684961	1.00[JPT][hapmap]
rs688030	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv33843	chr11:59908131-59945334	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs617135	MS4A4A	cis	multi-tissue	Pritchard
rs617135	SLC43A3	cis	parietal	SCAN
rs617135	DTX4	cis	parietal	SCAN
rs617135	GNG3	cis	parietal	SCAN
rs617135	FAM111A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59935600-59937200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr11:59935600-59937400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:59935600-59940400	Enhancers	HUVEC	blood vessel
4	chr11:59935800-59937000	ZNF genes & repeats	Spleen	Spleen
5	chr11:59935800-59947200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:59936000-59936800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr11:59936200-59936800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:59936200-59936800	Enhancers	HMEC	breast
9	chr11:59936200-59937800	Genic enhancers	Monocytes-CD14+_RO01746	blood
10	chr11:59936200-59938200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:59936400-59936800	Enhancers	Colonic Mucosa	Colon
12	chr11:59936400-59936800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr11:59936400-59937000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:59936400-59937000	ZNF genes & repeats	Dnd41	blood
15	chr11:59936400-59938600	Enhancers	Hela-S3	cervix
16	chr11:59936600-59937000	Enhancers	Adipose Nuclei	Adipose
17	chr11:59936600-59937200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood

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