Variant report

Variant	rs17408640
Chromosome Location	chr7:101631982-101631983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101631872..101634524-chr7:101635259..101637821,2	MCF-7	breast:
2	chr7:101628339..101629982-chr7:101630689..101633025,2	MCF-7	breast:
3	chr7:101611841..101614545-chr7:101629314..101633135,4	MCF-7	breast:
4	chr7:101630321..101633242-chr7:101633881..101635594,2	K562	blood:
5	chr7:101627337..101631221-chr7:101631346..101635612,7	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10231075	1.00[JPT][hapmap]
rs10231704	1.00[CHB][hapmap]
rs10236615	1.00[JPT][hapmap]
rs10243429	1.00[CHB][hapmap]
rs10245459	1.00[CHB][hapmap]
rs10246310	1.00[CHB][hapmap]
rs10249739	1.00[CHB][hapmap]
rs10252737	1.00[CHB][hapmap]
rs10259603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10261132	1.00[CHB][hapmap]
rs10276057	1.00[JPT][hapmap]
rs10488042	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10488043	1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10953355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953357	1.00[CHB][hapmap]
rs11769397	1.00[CHB][hapmap]
rs11975995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530931	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538286	1.00[CHB][hapmap]
rs17408612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17487076	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17487672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17495148	1.00[CHB][hapmap]
rs1882763	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202142	1.00[JPT][hapmap]
rs202147	1.00[JPT][hapmap]
rs202150	1.00[JPT][hapmap]
rs202152	1.00[JPT][hapmap]
rs2031085	1.00[JPT][hapmap]
rs28534780	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36118129	0.92[ASN][1000 genomes]
rs6465839	1.00[JPT][hapmap]
rs6465843	1.00[CHB][hapmap]
rs67101142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959475	1.00[CHB][hapmap]
rs6973312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6973714	0.92[ASN][1000 genomes]
rs73185836	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776498	1.00[CHB][hapmap]
rs7780375	0.92[ASN][1000 genomes]
rs7780631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7785266	1.00[JPT][hapmap]
rs7796818	1.00[JPT][hapmap]
rs7796995	1.00[JPT][hapmap]
rs7797764	1.00[CHB][hapmap]
rs7798358	1.00[CHB][hapmap]
rs7805379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7810922	1.00[JPT][hapmap]
rs9969318	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:101597000-101642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:101614400-101646400	Weak transcription	Fetal Brain Female	brain
4	chr7:101616400-101633000	Weak transcription	Gastric	stomach
5	chr7:101617000-101634000	Weak transcription	Liver	Liver
6	chr7:101620200-101642000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:101622200-101635600	Weak transcription	Pancreas	Pancrea
8	chr7:101625600-101635400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:101625600-101635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:101625800-101634200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:101627000-101632800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:101627000-101633400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:101627000-101633800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr7:101627000-101647400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:101627000-101671200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:101627800-101634400	Strong transcription	Fetal Intestine Small	intestine
17	chr7:101628000-101651600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:101628200-101632200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr7:101628400-101632600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:101628600-101632000	Enhancers	Right Ventricle	heart
21	chr7:101628600-101632800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:101628600-101633200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:101629000-101634000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:101629000-101651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:101629200-101632800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:101629400-101632600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:101629400-101633400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:101629600-101641400	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:101630000-101633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:101630000-101634400	Strong transcription	Fetal Stomach	stomach
31	chr7:101630000-101638000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:101630000-101641000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:101630000-101641200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:101630000-101641400	Weak transcription	Aorta	Aorta
35	chr7:101630000-101668000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:101630200-101633000	Genic enhancers	Thymus	Thymus
37	chr7:101630200-101633200	Genic enhancers	Fetal Thymus	thymus
38	chr7:101630200-101634200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:101630400-101633000	Genic enhancers	Dnd41	blood
40	chr7:101630400-101633200	Strong transcription	Lung	lung
41	chr7:101630400-101635400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr7:101630400-101640000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:101630400-101641200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:101630400-101643800	Weak transcription	Right Atrium	heart
45	chr7:101630400-101646600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:101630600-101632400	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:101630600-101632400	Weak transcription	Left Ventricle	heart
48	chr7:101630600-101633000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:101630600-101633000	Genic enhancers	GM12878-XiMat	blood
50	chr7:101630600-101634000	Weak transcription	Duodenum Mucosa	Duodenum

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