Variant report

Variant	rs16876340
Chromosome Location	chr6:86225060-86225061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86333196..86333767-chr6:86224978..86225478,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000068654	Chromatin interaction
ENSG00000132300	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13194512	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13198956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13202606	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16876230	0.84[EUR][1000 genomes]
rs16876385	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34239697	0.91[EUR][1000 genomes]
rs34898046	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34936540	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35121980	0.87[EUR][1000 genomes]
rs35367106	0.91[EUR][1000 genomes]
rs35694036	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35712823	0.87[EUR][1000 genomes]
rs35988746	0.83[EUR][1000 genomes]
rs36088473	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734442	0.85[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];1.00[EUR][1000 genomes]
rs3900740	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707206	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707213	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55648312	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55810446	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67493405	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906121	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6909402	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6909654	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6910641	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6915519	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71570763	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71570764	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71570766	0.91[EUR][1000 genomes]
rs7738371	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740830	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742792	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766863	0.86[ASN][1000 genomes]
rs7771577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450302	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
15	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
3	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
4	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
5	chr6:86211400-86246400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:86212000-86228600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:86212000-86246600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:86215800-86227600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:86216000-86225400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr6:86216200-86225600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:86218000-86260200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:86218600-86226000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:86219200-86227600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr6:86219200-86246200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:86219400-86225200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:86219400-86227600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:86219600-86227600	Strong transcription	Dnd41	blood
19	chr6:86219800-86225200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:86219800-86225200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:86220200-86252400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:86220200-86257200	Weak transcription	Fetal Heart	heart
23	chr6:86221000-86245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:86221400-86242800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
26	chr6:86222200-86232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:86222200-86232400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:86222200-86249800	Weak transcription	Aorta	Aorta
29	chr6:86222400-86229200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:86222600-86225400	Weak transcription	A549	lung
31	chr6:86222600-86229200	Weak transcription	Fetal Intestine Small	intestine
32	chr6:86222600-86233200	Weak transcription	Fetal Stomach	stomach
33	chr6:86222600-86243800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:86222800-86229600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:86223000-86225200	Strong transcription	HUVEC	blood vessel
37	chr6:86223000-86242600	Weak transcription	Right Ventricle	heart
38	chr6:86223200-86231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:86223200-86231000	Weak transcription	Ovary	ovary
40	chr6:86223200-86233200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:86223200-86235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:86223200-86242200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:86223200-86242200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:86223200-86242600	Weak transcription	Psoas Muscle	Psoas
45	chr6:86223200-86242600	Weak transcription	Thymus	Thymus
46	chr6:86223200-86243000	Weak transcription	Brain Angular Gyrus	brain
47	chr6:86223200-86260200	Weak transcription	Lung	lung
48	chr6:86223400-86226400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:86223400-86227200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:86223400-86229000	Weak transcription	Fetal Intestine Large	intestine

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