Variant report

Variant	rs4342423
Chromosome Location	chr6:33732679-33732680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33724946..33727778-chr6:33732399..33734777,2	MCF-7	breast:
2	chr6:33731707..33733377-chr6:33739681..33741307,2	K562	blood:
3	chr6:33683155..33686367-chr6:33732476..33736646,4	MCF-7	breast:
4	chr6:33730312..33733510-chr6:33847562..33850265,3	K562	blood:
5	chr6:33732354..33734796-chr6:33734914..33737120,3	K562	blood:
6	chr6:33587894..33590790-chr6:33732523..33735377,2	MCF-7	breast:
7	chr6:33677635..33679706-chr6:33732667..33735011,2	K562	blood:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11752297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359781	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013365	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013381	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296743	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296746	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296747	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296748	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793079	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806109	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806110	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4711347	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4711351	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713681	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713682	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713683	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4713684	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6904716	0.88[CHB][hapmap]
rs6904991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920075	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925273	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747695	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751726	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751728	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs755496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756137	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9366829	0.82[JPT][hapmap]
rs9380376	0.80[CEU][hapmap];0.88[JPT][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9380378	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394166	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394168	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs943467	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs943477	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4342423	C6orf125	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:33729000-33736200	Weak transcription	HSMM	muscle
5	chr6:33729800-33734800	Weak transcription	HSMMtube	muscle
6	chr6:33730000-33738600	Weak transcription	A549	lung
7	chr6:33730200-33733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:33730200-33736400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:33730200-33737800	Weak transcription	Right Atrium	heart
10	chr6:33730200-33738200	Weak transcription	Colonic Mucosa	Colon
11	chr6:33730200-33738400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:33730800-33736000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:33730800-33736600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:33730800-33737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:33730800-33738600	Weak transcription	Liver	Liver
17	chr6:33731400-33738400	Weak transcription	Spleen	Spleen
18	chr6:33731600-33738200	Weak transcription	Right Ventricle	heart
19	chr6:33731800-33733200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:33731800-33735400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:33732000-33736200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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