Variant report

Variant	rs7759796
Chromosome Location	chr6:25322301-25322302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25302209..25304566-chr6:25321319..25323421,2	MCF-7	breast:
2	chr6:25315748..25318380-chr6:25321578..25323806,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12055697	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs16890366	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1883393	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2143023	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690042	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2744287	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4712904	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs4712905	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4712906	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4712907	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs55967593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55999195	0.82[ASN][1000 genomes]
rs58191968	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs60084615	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6456664	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6456665	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6456666	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6456668	0.81[ASN][1000 genomes]
rs6903148	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6906812	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913606	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6913886	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6914439	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6914514	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6914654	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6914798	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6914930	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6915270	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6917631	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6921343	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6923529	0.87[ASN][1000 genomes]
rs6927238	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6938281	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6938594	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs730711	0.89[ASN][1000 genomes]
rs73392399	0.87[ASN][1000 genomes]
rs73396126	0.91[ASN][1000 genomes]
rs7741580	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743750	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7746942	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7746969	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7755701	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7756143	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7758529	0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7759828	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759879	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7764111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295654	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9295655	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9348671	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9348672	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9356974	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9356975	0.90[JPT][hapmap]
rs9366616	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9366617	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9366618	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9379752	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9379753	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9379754	0.85[CHB][hapmap]
rs9393639	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461132	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9461134	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9461135	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9461136	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9467466	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs999039	0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
4	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
5	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
11	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
13	chr6:25316200-25326800	Weak transcription	Gastric	stomach
14	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
15	chr6:25316600-25324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:25317200-25324200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:25317200-25324200	Weak transcription	Aorta	Aorta
18	chr6:25317400-25324000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:25318600-25324200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:25318600-25324400	Weak transcription	Lung	lung
21	chr6:25319000-25324200	Weak transcription	Ovary	ovary
22	chr6:25319000-25324200	Weak transcription	Right Atrium	heart
23	chr6:25319200-25324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:25319400-25324200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:25319400-25324200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:25319800-25324200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:25320600-25324200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:25321000-25324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:25321000-25324200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:25321000-25324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:25321000-25324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:25321000-25324200	Weak transcription	A549	lung
33	chr6:25321000-25324200	Weak transcription	Osteobl	bone
34	chr6:25321000-25324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:25321000-25329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:25321000-25329600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:25321000-25331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:25321200-25324000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:25321200-25324200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:25321200-25326000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:25321200-25329200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:25321200-25329400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:25321200-25329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:25321600-25324200	Weak transcription	HSMMtube	muscle
45	chr6:25321600-25324400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:25321600-25325200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:25321600-25329200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:25321600-25329400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:25321600-25329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:25321600-25329800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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