Variant report

Variant	rs7847479
Chromosome Location	chr9:102622237-102622238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102620386..102622308-chr9:102623270..102626025,2	MCF-7	breast:
2	chr9:102612792..102615430-chr9:102621366..102623086,2	MCF-7	breast:
3	chr9:102614101..102615625-chr9:102620397..102622251,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081715	0.92[ASN][1000 genomes]
rs10739788	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs10739789	0.93[ASN][1000 genomes]
rs10739790	0.91[ASN][1000 genomes]
rs10760696	0.95[ASN][1000 genomes]
rs10760697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs10819699	0.97[ASN][1000 genomes]
rs10819701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10819702	0.95[ASN][1000 genomes]
rs10819703	0.94[ASN][1000 genomes]
rs10819704	0.93[ASN][1000 genomes]
rs10988910	0.95[ASN][1000 genomes]
rs10988912	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs10988913	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10988914	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10988916	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1131339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12353310	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12555147	0.82[ASN][1000 genomes]
rs12686676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13299746	0.96[ASN][1000 genomes]
rs2416878	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2416939	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4265238	0.85[ASN][1000 genomes]
rs4742776	0.89[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4743366	0.94[ASN][1000 genomes]
rs4743367	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs4743368	0.88[ASN][1000 genomes]
rs56004327	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6478986	0.93[ASN][1000 genomes]
rs7023690	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024182	0.94[ASN][1000 genomes]
rs7024294	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7032301	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034892	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040578	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs7042795	0.93[ASN][1000 genomes]
rs7870031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs7871142	0.90[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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102595400-102628200	Weak transcription	Fetal Brain Female	brain
2	chr9:102609800-102627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:102610400-102631200	Weak transcription	NHLF	lung
4	chr9:102610400-102644000	Weak transcription	Aorta	Aorta
5	chr9:102611400-102627000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:102611800-102628800	Weak transcription	Right Ventricle	heart
7	chr9:102612800-102628200	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:102613400-102626200	Weak transcription	Gastric	stomach
9	chr9:102613400-102628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:102613800-102625200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:102614400-102626800	Weak transcription	Thymus	Thymus
12	chr9:102614400-102627600	Weak transcription	Primary T cells from cord blood	blood
13	chr9:102615000-102627600	Weak transcription	Psoas Muscle	Psoas
14	chr9:102615400-102625400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:102615400-102625800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:102615400-102626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:102615400-102628600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:102615400-102644000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:102617400-102628200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:102617400-102629000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:102618200-102628800	Weak transcription	Left Ventricle	heart
22	chr9:102618600-102622400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:102620400-102623200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:102621400-102622400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:102621400-102623200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:102621800-102622800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr9:102621800-102623000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:102621800-102623200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:102622000-102622600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:102622000-102623000	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:102622000-102623200	Enhancers	Brain Germinal Matrix	brain
32	chr9:102622000-102625400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:102622000-102626600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:102622000-102628800	Weak transcription	Ovary	ovary
35	chr9:102622000-102630000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:102622200-102622600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:102622200-102623200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:102622200-102625200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:102622200-102625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:102622200-102625400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:102622200-102625400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:102622200-102628800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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