Variant report

Variant	rs9403383
Chromosome Location	chr6:142694049-142694050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142692998..142695094-chr6:142697780..142699490,2	MCF-7	breast:
2	chr6:142681414..142683380-chr6:142691600..142694541,2	MCF-7	breast:
3	chr6:142686552..142689660-chr6:142691331..142695100,3	MCF-7	breast:
4	chr6:142621406..142625298-chr6:142688620..142694485,6	MCF-7	breast:
5	chr6:142693095..142695655-chr6:142695797..142698299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1040525	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040526	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1342060	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs1360194	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418201	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155259	0.86[EUR][1000 genomes]
rs1891308	0.81[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2039986	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2039987	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs2050157	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294764	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294771	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs262119	0.86[EUR][1000 genomes]
rs262121	0.86[EUR][1000 genomes]
rs262129	0.86[EUR][1000 genomes]
rs263178	0.85[EUR][1000 genomes]
rs263179	0.85[EUR][1000 genomes]
rs263180	0.86[EUR][1000 genomes]
rs263181	0.86[EUR][1000 genomes]
rs263182	0.86[EUR][1000 genomes]
rs263183	0.86[EUR][1000 genomes]
rs263184	0.86[EUR][1000 genomes]
rs263185	0.84[EUR][1000 genomes]
rs263186	0.86[EUR][1000 genomes]
rs263187	0.86[EUR][1000 genomes]
rs263188	0.86[EUR][1000 genomes]
rs263189	0.86[EUR][1000 genomes]
rs3748069	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3817929	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4896582	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs611802	0.83[EUR][1000 genomes]
rs6570507	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570508	0.80[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6570509	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570510	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6909857	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6929442	0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6937121	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741741	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753012	0.82[GIH][hapmap];0.93[TSI][hapmap]
rs7754638	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7755109	0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7756305	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs7763064	0.91[EUR][1000 genomes]
rs7770386	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7774095	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776375	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9373346	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9389984	0.89[EUR][1000 genomes]
rs9389985	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9389986	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389987	0.92[EUR][1000 genomes]
rs9399401	0.83[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9403380	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403381	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9403382	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403387	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9496346	0.94[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496369	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496374	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9496392	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs962554	0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs972982	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142681000-142695200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:142682600-142694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:142682800-142694600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:142689400-142696000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:142691600-142695200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:142692000-142695600	Weak transcription	Fetal Lung	lung
7	chr6:142692800-142696200	Enhancers	HUVEC	blood vessel
8	chr6:142693000-142696200	Enhancers	NHEK	skin
9	chr6:142693200-142694800	Genic enhancers	HepG2	liver
10	chr6:142693200-142696800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:142693200-142700000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:142693200-142700200	Enhancers	HMEC	breast
13	chr6:142693200-142700600	Enhancers	Hela-S3	cervix
14	chr6:142693400-142694400	Enhancers	HSMM	muscle
15	chr6:142693400-142694800	Enhancers	Stomach Mucosa	stomach
16	chr6:142693400-142696200	Enhancers	Fetal Intestine Large	intestine
17	chr6:142693400-142696600	Enhancers	Fetal Intestine Small	intestine
18	chr6:142693600-142694200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:142693600-142694200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:142693600-142694400	Enhancers	NHLF	lung
21	chr6:142693600-142694600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:142693600-142694800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:142693600-142694800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:142693600-142695400	Enhancers	Small Intestine	intestine
25	chr6:142693600-142696200	Enhancers	Liver	Liver
26	chr6:142693800-142694400	Transcr. at gene 5' and 3'	A549	lung
27	chr6:142693800-142695600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:142693800-142696400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:142694000-142694200	Enhancers	Fetal Kidney	kidney
30	chr6:142694000-142694400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:142694000-142695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:142694000-142695200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:142694000-142695200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:142694000-142695400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:142694000-142695400	Weak transcription	NH-A	brain
36	chr6:142694000-142695600	Weak transcription	Placenta	Placenta
37	chr6:142694000-142695600	Weak transcription	HSMMtube	muscle
38	chr6:142694000-142696000	Weak transcription	NHDF-Ad	bronchial
39	chr6:142694000-142696000	Weak transcription	Osteobl	bone
40	chr6:142694000-142698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:142694000-142699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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