Variant report

Variant	rs9403116
Chromosome Location	chr6:140085106-140085107
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140081301..140083675-chr6:140083815..140085974,2	MCF-7	breast:
2	chr6:140028951..140031620-chr6:140084219..140086898,2	K562	blood:
3	chr6:140055856..140059094-chr6:140083948..140086975,3	K562	blood:
4	chr6:139694058..139697860-chr6:140083167..140088670,5	MCF-7	breast:
5	chr6:140077496..140081190-chr6:140083108..140086275,5	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10499213	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10499214	0.98[ASN][1000 genomes]
rs11962730	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11963532	0.99[ASN][1000 genomes]
rs11964275	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12055436	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055472	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055843	0.88[ASN][1000 genomes]
rs12662206	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12664473	0.94[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs17069206	0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs17069225	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1936210	0.88[ASN][1000 genomes]
rs1936214	0.98[ASN][1000 genomes]
rs2096283	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2096284	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2154032	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2185923	0.87[ASN][1000 genomes]
rs2327993	0.87[ASN][1000 genomes]
rs4520026	0.98[ASN][1000 genomes]
rs4535566	0.85[ASN][1000 genomes]
rs55764205	0.88[ASN][1000 genomes]
rs55966840	0.98[ASN][1000 genomes]
rs60350063	0.99[ASN][1000 genomes]
rs60758082	0.88[ASN][1000 genomes]
rs6570372	0.88[ASN][1000 genomes]
rs6570373	0.89[ASN][1000 genomes]
rs6570374	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6901783	0.93[JPT][hapmap]
rs6905478	0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs6933318	0.93[JPT][hapmap]
rs73556090	0.87[ASN][1000 genomes]
rs73558032	0.99[ASN][1000 genomes]
rs7743796	0.98[ASN][1000 genomes]
rs7752001	0.82[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7752323	0.88[ASN][1000 genomes]
rs7756866	0.98[ASN][1000 genomes]
rs7769567	0.97[ASN][1000 genomes]
rs7774968	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9321752	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373246	0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373247	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9373248	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9376452	0.87[JPT][hapmap]
rs9376457	0.88[ASN][1000 genomes]
rs9376463	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9376464	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9385874	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9385875	0.98[ASN][1000 genomes]
rs9385876	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389715	0.88[ASN][1000 genomes]
rs9389717	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399292	0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403113	0.87[ASN][1000 genomes]
rs9403114	0.98[ASN][1000 genomes]
rs9403115	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv464065	chr6:140027836-140085873	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv604766	chr6:140027836-140085873	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140070200-140085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:140073000-140089400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:140075000-140085400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:140076000-140085200	Weak transcription	Left Ventricle	heart
5	chr6:140076400-140085200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:140076800-140085200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:140077000-140085800	Weak transcription	Fetal Kidney	kidney
8	chr6:140077400-140085800	Weak transcription	Pancreas	Pancrea
9	chr6:140079400-140085200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:140079600-140085400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:140079800-140090400	Weak transcription	Aorta	Aorta
12	chr6:140081200-140085400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:140081400-140085600	Weak transcription	Ovary	ovary
14	chr6:140082400-140085600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:140082400-140089400	Weak transcription	Psoas Muscle	Psoas
16	chr6:140083000-140086600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:140083200-140085200	Enhancers	Osteobl	bone
18	chr6:140083200-140085400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:140083200-140085800	Enhancers	NHDF-Ad	bronchial
20	chr6:140083200-140086400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:140083200-140086400	Enhancers	Fetal Heart	heart
22	chr6:140083200-140087400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:140083200-140088200	Enhancers	HSMM	muscle
24	chr6:140083400-140085400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:140083400-140085400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:140083400-140088200	Enhancers	HSMMtube	muscle
27	chr6:140083400-140090200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:140083600-140085800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:140083600-140086200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:140083600-140087800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:140083600-140087800	Enhancers	Hela-S3	cervix
32	chr6:140083600-140087800	Enhancers	HUVEC	blood vessel
33	chr6:140083600-140088200	Enhancers	K562	blood
34	chr6:140083800-140085200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:140083800-140085800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:140083800-140085800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:140083800-140087600	Enhancers	NH-A	brain
38	chr6:140083800-140087800	Enhancers	NHLF	lung
39	chr6:140084000-140085200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:140084000-140089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:140084200-140085200	Weak transcription	GM12878-XiMat	blood
42	chr6:140084200-140085600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:140084200-140085800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:140084200-140086200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:140084400-140085200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr6:140084400-140085600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:140084600-140085800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr6:140084600-140087600	Enhancers	HMEC	breast
49	chr6:140084800-140086000	Weak transcription	Primary B cells from cord blood	blood
50	chr6:140085000-140085200	Enhancers	Right Atrium	heart

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