Variant report

Variant	rs2395449
Chromosome Location	chr6:33728755-33728756
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:33674794..33680843-chr6:33726905..33731016,6	MCF-7	breast:
2	chr6:33727358..33730164-chr6:33732846..33736236,4	K562	blood:
3	chr6:33728239..33730038-chr6:33992593..33994238,2	MCF-7	breast:
4	chr6:33728564..33732066-chr6:33733725..33737558,5	MCF-7	breast:
5	chr6:33727069..33729812-chr6:33754645..33756635,3	MCF-7	breast:
6	chr6:33724784..33727400-chr6:33728214..33730024,2	MCF-7	breast:
7	chr6:33708694..33710403-chr6:33728367..33730684,2	MCF-7	breast:
8	chr6:33710878..33712572-chr6:33728483..33730415,2	K562	blood:
9	chr6:33717929..33721430-chr6:33728075..33731260,3	MCF-7	breast:
10	chr6:33557463..33558024-chr6:33728236..33728791,2	K562	blood:
11	chr6:33684753..33687394-chr6:33728535..33731247,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11752297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359781	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2013365	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2013381	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296743	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296746	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296747	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296748	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793079	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806108	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806109	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806110	0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4342423	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]
rs4711351	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713681	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713682	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713683	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713684	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6904716	0.88[CHB][hapmap]
rs6904991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6920075	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925273	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747695	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs751726	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs751728	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs755496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs756137	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9366829	0.82[JPT][hapmap]
rs9380376	0.81[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9380378	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9394165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394166	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394168	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs943467	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs943477	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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
rs2395449	C6orf125	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 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	chr6:33715600-33729400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:33719600-33729000	Weak transcription	Right Atrium	heart
4	chr6:33719800-33729200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:33720200-33730600	Weak transcription	Spleen	Spleen
6	chr6:33720600-33729400	Weak transcription	Fetal Intestine Large	intestine
7	chr6:33721000-33729400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:33723400-33729800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:33723600-33728800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:33723600-33729000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:33724000-33730200	Enhancers	Stomach Mucosa	stomach
13	chr6:33725000-33728800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:33725200-33729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:33725200-33729600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:33725200-33729800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:33726000-33731000	Enhancers	Fetal Stomach	stomach
18	chr6:33726200-33729600	Enhancers	Liver	Liver
19	chr6:33726200-33731000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:33726200-33731400	Enhancers	Fetal Lung	lung
21	chr6:33726400-33729200	Weak transcription	Placenta	Placenta
22	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:33727000-33730800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:33727200-33729000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:33727400-33728800	Weak transcription	A549	lung
26	chr6:33727800-33729000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr6:33727800-33729600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:33728000-33729000	Enhancers	Fetal Kidney	kidney
29	chr6:33728000-33729200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:33728000-33729200	Bivalent Enhancer	HepG2	liver
31	chr6:33728000-33730000	Weak transcription	Hela-S3	cervix
32	chr6:33728000-33730200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:33728000-33730800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:33728000-33731400	Enhancers	Fetal Muscle Leg	muscle
35	chr6:33728000-33732000	Enhancers	Fetal Muscle Trunk	muscle
36	chr6:33728200-33728800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:33728200-33728800	Weak transcription	HSMM	muscle
38	chr6:33728200-33729000	Weak transcription	Left Ventricle	heart
39	chr6:33728200-33730400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:33728400-33729600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:33728600-33728800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:33728600-33728800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr6:33728600-33730000	Enhancers	Fetal Thymus	thymus
44	chr6:33728600-33730600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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