Variant report

Variant	rs16867976
Chromosome Location	chr6:27724986-27724987
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27670250..27673191-chr6:27723819..27726632,2	K562	blood:
2	chr6:27106999..27109388-chr6:27723167..27725531,2	MCF-7	breast:
3	chr6:27720750..27725347-chr6:27727186..27730834,4	MCF-7	breast:
4	chr6:27115174..27117346-chr6:27724158..27725816,2	K562	blood:

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction
ENSG00000198339	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1028311	0.87[CHB][hapmap]
rs10484400	0.95[EUR][1000 genomes]
rs10946943	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs1157432	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12055685	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs12173985	0.91[EUR][1000 genomes]
rs12174087	0.90[EUR][1000 genomes]
rs12663707	0.95[EUR][1000 genomes]
rs12664599	0.95[EUR][1000 genomes]
rs1555021	0.91[EUR][1000 genomes]
rs1565334	0.80[CHB][hapmap]
rs16867886	0.91[EUR][1000 genomes]
rs16867916	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs16867921	0.93[EUR][1000 genomes]
rs16867983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16868156	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1973889	0.91[EUR][1000 genomes]
rs2142704	0.87[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs3175123	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3800321	0.86[CHB][hapmap]
rs56408767	0.91[EUR][1000 genomes]
rs59893892	0.93[EUR][1000 genomes]
rs60096640	0.81[EUR][1000 genomes]
rs6906653	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs6920044	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs73385147	0.91[EUR][1000 genomes]
rs73385152	0.91[EUR][1000 genomes]
rs73385154	0.91[EUR][1000 genomes]
rs7753236	0.93[EUR][1000 genomes]
rs878241	0.91[EUR][1000 genomes]
rs9295751	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs9348771	0.91[EUR][1000 genomes]
rs9348777	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348778	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357043	0.91[EUR][1000 genomes]
rs9357044	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs9357048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368517	0.90[EUR][1000 genomes]
rs9368521	0.91[EUR][1000 genomes]
rs9368524	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs9368525	0.88[EUR][1000 genomes]
rs9368526	0.95[EUR][1000 genomes]
rs9368538	0.80[CHB][hapmap];1.00[YRI][hapmap]
rs9380000	0.90[EUR][1000 genomes]
rs9380001	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs9380005	0.88[EUR][1000 genomes]
rs9380022	0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs9380024	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9393826	0.88[CHB][hapmap]
rs9393832	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs9393842	0.91[EUR][1000 genomes]
rs9393849	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393852	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393856	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9393865	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27721200-27725000	Weak transcription	Esophagus	oesophagus
2	chr6:27721200-27725000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:27721200-27725200	Weak transcription	Gastric	stomach
4	chr6:27722000-27725000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:27722000-27725200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27722200-27725000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:27722200-27725000	Weak transcription	Colonic Mucosa	Colon
8	chr6:27722200-27725000	Weak transcription	Placenta	Placenta
9	chr6:27722200-27725000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:27722200-27725200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:27722400-27725000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:27722400-27725000	Weak transcription	Fetal Intestine Large	intestine
13	chr6:27722400-27725000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:27722400-27725000	Weak transcription	Right Atrium	heart
15	chr6:27722600-27725000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:27722600-27728000	Weak transcription	Hela-S3	cervix
17	chr6:27724200-27726200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:27724400-27725000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:27724400-27725000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:27724400-27725000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:27724400-27725200	Flanking Active TSS	Dnd41	blood
22	chr6:27724400-27725200	Weak transcription	K562	blood
23	chr6:27724600-27725000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:27724600-27725000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr6:27724600-27725000	Enhancers	Fetal Lung	lung
26	chr6:27724600-27725000	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:27724600-27725400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:27724600-27726000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:27724600-27726000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:27724800-27725000	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr6:27724800-27725000	Active TSS	Primary hematopoietic stem cells	blood
32	chr6:27724800-27725000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:27724800-27725000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr6:27724800-27725000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:27724800-27725000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:27724800-27725000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:27724800-27725000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:27724800-27725000	Enhancers	Fetal Intestine Small	intestine
39	chr6:27724800-27725000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
40	chr6:27724800-27725000	Active TSS	Ovary	ovary
41	chr6:27724800-27725000	Enhancers	HMEC	breast
42	chr6:27724800-27725200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
43	chr6:27724800-27725200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:27724800-27725200	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr6:27724800-27725200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:27724800-27725200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:27724800-27725200	Active TSS	Brain Anterior Caudate	brain
48	chr6:27724800-27725200	Active TSS	Colon Smooth Muscle	Colon
49	chr6:27724800-27725200	Bivalent/Poised TSS	Thymus	Thymus
50	chr6:27724800-27725200	Flanking Active TSS	NHEK	skin

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