Variant report

Variant	rs6904716
Chromosome Location	chr6:33741289-33741290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33731707..33733377-chr6:33739681..33741307,2	K562	blood:
2	chr6:33733565..33735382-chr6:33741109..33742921,2	K562	blood:
3	chr6:33736395..33737905-chr6:33740079..33742724,2	K562	blood:
4	chr6:33677854..33679623-chr6:33741154..33743087,2	MCF-7	breast:
5	chr6:33697484..33700204-chr6:33739217..33741356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1075379	0.89[YRI][hapmap]
rs11752297	0.88[CHB][hapmap]
rs12524768	0.92[YRI][hapmap]
rs1359781	0.94[CHB][hapmap]
rs2281819	0.87[JPT][hapmap]
rs2296743	0.81[CHB][hapmap]
rs2296748	0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap]
rs2395449	0.88[CHB][hapmap]
rs2894342	0.87[JPT][hapmap]
rs3763253	0.87[JPT][hapmap]
rs3793079	0.88[CHB][hapmap]
rs3806108	0.88[CHB][hapmap]
rs3806109	0.81[CHB][hapmap]
rs4342423	0.88[CHB][hapmap]
rs4711345	0.87[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs4713677	0.87[JPT][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs6904991	0.88[CHB][hapmap]
rs751096	1.00[YRI][hapmap]
rs755496	0.88[CHB][hapmap]
rs755497	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs767896	0.93[JPT][hapmap]
rs7755323	0.93[YRI][hapmap]
rs9380376	0.82[JPT][hapmap]
rs9394165	0.88[CHB][hapmap]
rs9394166	0.94[CHB][hapmap]
rs943467	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6904716	C6orf125	cis	cerebellum	SCAN
rs6904716	SLC12A6	trans	parietal	SCAN
rs6904716	DEF6	cis	parietal	SCAN
rs6904716	MDGA1	cis	cerebellum	SCAN
rs6904716	C6orf227	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:33736800-33743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:33737800-33742600	Weak transcription	Hela-S3	cervix
4	chr6:33738600-33741400	Genic enhancers	Fetal Stomach	stomach
5	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
6	chr6:33738800-33741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:33738800-33741800	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr6:33739000-33741400	Enhancers	Fetal Brain Male	brain
9	chr6:33739000-33741400	Enhancers	HSMM	muscle
10	chr6:33739000-33741600	Enhancers	HSMMtube	muscle
11	chr6:33739000-33746000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:33739600-33741400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:33739600-33742000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:33739800-33741400	Genic enhancers	Placenta	Placenta
17	chr6:33739800-33741600	Genic enhancers	Esophagus	oesophagus
18	chr6:33739800-33741600	Genic enhancers	Fetal Muscle Leg	muscle
19	chr6:33739800-33741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:33739800-33741800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:33739800-33741800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:33739800-33741800	Genic enhancers	Brain Hippocampus Middle	brain
23	chr6:33739800-33741800	Genic enhancers	NHLF	lung
24	chr6:33739800-33742000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:33739800-33742000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:33739800-33742400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:33739800-33742600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
32	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:33740000-33741400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:33740000-33741400	Genic enhancers	Fetal Lung	lung
36	chr6:33740000-33741800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:33740000-33741800	Genic enhancers	NHEK	skin
38	chr6:33740000-33742400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:33740000-33746000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:33740000-33749000	Strong transcription	Brain Anterior Caudate	brain
41	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:33740000-33752800	Strong transcription	Dnd41	blood
45	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:33740000-33753000	Strong transcription	HepG2	liver
47	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:33740200-33741600	Genic enhancers	Muscle Satellite Cultured Cells	--

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