Variant report

Variant	rs7025563
Chromosome Location	chr9:110078582-110078583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110045249..110048106-chr9:110077151..110079767,3	MCF-7	breast:
2	chr9:110070353..110073170-chr9:110078217..110082315,4	MCF-7	breast:
3	chr9:110044399..110049612-chr9:110071012..110080286,12	K562	blood:
4	chr9:110044605..110047075-chr9:110077754..110080578,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10113916	0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs10481632	0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10521083	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10732368	0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739234	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10739236	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10739238	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10759222	0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs10759223	0.89[ASN][1000 genomes]
rs10759225	0.80[CHB][hapmap];0.83[ASN][1000 genomes]
rs10759226	0.92[ASN][1000 genomes]
rs10759227	0.81[ASN][1000 genomes]
rs10816483	0.82[ASN][1000 genomes]
rs10816485	0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10816486	0.89[ASN][1000 genomes]
rs10816487	0.88[ASN][1000 genomes]
rs10816490	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10816491	0.86[EUR][1000 genomes]
rs10816492	0.83[ASN][1000 genomes]
rs10816493	0.98[ASN][1000 genomes]
rs10978791	0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10978798	0.97[ASN][1000 genomes]
rs1323806	0.80[CHB][hapmap]
rs1323808	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1323809	0.80[CHB][hapmap];0.83[ASN][1000 genomes]
rs1535765	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1805329	0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs1805332	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1805334	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805335	0.80[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs1886134	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969798	0.93[ASN][1000 genomes]
rs1980725	0.94[ASN][1000 genomes]
rs2147071	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2147072	0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2417783	0.85[ASN][1000 genomes]
rs2417784	0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2417785	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs28534368	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3818367	0.98[ASN][1000 genomes]
rs4278207	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4625087	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4978404	0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978406	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978844	0.98[ASN][1000 genomes]
rs4978849	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61701375	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs698475	0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs7019341	1.00[ASN][1000 genomes]
rs7029997	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7030169	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7030555	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7030631	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7031906	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7035611	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7035725	0.84[ASN][1000 genomes]
rs7038737	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7039041	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7041497	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7043962	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7046950	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7856112	0.92[ASN][1000 genomes]
rs7856227	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7859769	0.92[ASN][1000 genomes]
rs817836	0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs817839	0.80[AFR][1000 genomes]
rs817840	0.83[JPT][hapmap];0.80[AFR][1000 genomes]
rs817841	0.83[JPT][hapmap];0.80[AFR][1000 genomes]
rs817844	0.80[AFR][1000 genomes]
rs817845	0.80[AFR][1000 genomes]
rs942292	0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs942293	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9632893	0.80[AFR][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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:110057200-110079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
4	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:110062400-110078600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:110062600-110078800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:110063000-110079200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:110063600-110078600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:110063800-110079200	Strong transcription	Osteobl	bone
10	chr9:110063800-110079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:110064000-110085000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:110065200-110089200	Strong transcription	Fetal Thymus	thymus
13	chr9:110065600-110098600	Strong transcription	Dnd41	blood
14	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:110070400-110085000	Weak transcription	Colonic Mucosa	Colon
16	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:110070600-110079400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:110071400-110084000	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
20	chr9:110071800-110079800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:110071800-110084400	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:110073800-110080000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:110074200-110082600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:110074200-110083000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr9:110074200-110083200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:110074200-110088200	Strong transcription	Fetal Intestine Large	intestine
27	chr9:110075000-110079000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:110075000-110079200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:110075000-110079200	Strong transcription	HSMM	muscle
30	chr9:110075000-110079200	Weak transcription	HSMMtube	muscle
31	chr9:110075000-110080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:110075000-110084800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:110075000-110088000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:110075200-110079200	Weak transcription	Brain Angular Gyrus	brain
35	chr9:110075200-110079200	Weak transcription	Pancreas	Pancrea
36	chr9:110075200-110079200	Weak transcription	Psoas Muscle	Psoas
37	chr9:110075200-110079200	Weak transcription	Right Atrium	heart
38	chr9:110075200-110079600	Weak transcription	Aorta	Aorta
39	chr9:110075200-110084800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:110075200-110084800	Weak transcription	Spleen	Spleen
41	chr9:110075200-110090600	Weak transcription	Right Ventricle	heart
42	chr9:110075200-110093400	Weak transcription	Esophagus	oesophagus
43	chr9:110075400-110079200	Weak transcription	Ovary	ovary
44	chr9:110075800-110079200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:110075800-110079200	Weak transcription	Gastric	stomach
46	chr9:110076000-110089400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:110076200-110079200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:110076200-110079400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr9:110076200-110084600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:110076200-110087800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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