Variant report

Variant	rs9561939
Chromosome Location	chr13:96367727-96367728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96327826..96331109-chr13:96365382..96368282,3	MCF-7	breast:
2	chr13:96367268..96370251-chr13:96370563..96373311,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247400	Chromatin interaction
ENSG00000102580	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12430152	0.89[YRI][hapmap]
rs12583795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12583796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12855055	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17885081	0.85[AFR][1000 genomes]
rs2389530	0.80[CHB][hapmap]
rs3099357	0.80[CHB][hapmap]
rs3099359	0.80[CHB][hapmap]
rs3101570	0.96[YRI][hapmap]
rs34205636	0.81[AMR][1000 genomes]
rs35740456	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3886352	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3901894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4409947	0.93[YRI][hapmap]
rs59576762	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492820	0.90[CHB][hapmap]
rs6492821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7316996	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7318892	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs7323408	0.90[YRI][hapmap]
rs7331211	0.82[YRI][hapmap]
rs7331549	0.90[YRI][hapmap]
rs7334552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7338266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7983756	0.86[CHB][hapmap]
rs7991405	0.96[YRI][hapmap]
rs7995306	0.92[CEU][hapmap]
rs9302084	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561925	0.89[CEU][hapmap]
rs9561931	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561935	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9561936	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9561953	0.92[CEU][hapmap]
rs9584324	0.96[YRI][hapmap]
rs9584326	0.90[JPT][hapmap]
rs9590310	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96347000-96377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:96351000-96368600	Weak transcription	Lung	lung
3	chr13:96356000-96372400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:96356600-96393600	Weak transcription	Right Ventricle	heart
5	chr13:96359400-96386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:96359800-96368000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:96359800-96379200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:96360400-96369400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:96360600-96379200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:96360600-96383000	Weak transcription	K562	blood
11	chr13:96360600-96384000	Weak transcription	Small Intestine	intestine
12	chr13:96360800-96374400	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:96361000-96368600	Weak transcription	Pancreas	Pancrea
14	chr13:96361000-96371000	Weak transcription	Aorta	Aorta
15	chr13:96361000-96380600	Weak transcription	Fetal Heart	heart
16	chr13:96361000-96393600	Weak transcription	Spleen	Spleen
17	chr13:96361200-96368400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:96362200-96371200	Strong transcription	Primary T cells from cord blood	blood
19	chr13:96362400-96385800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:96362800-96393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:96363200-96375600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:96363200-96380000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:96364200-96386200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr13:96364600-96384400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:96364600-96385400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:96364800-96377400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:96365000-96368600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr13:96365000-96368600	Weak transcription	Esophagus	oesophagus
29	chr13:96365200-96367800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr13:96365200-96368000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:96365400-96367800	Enhancers	NHDF-Ad	bronchial
32	chr13:96365400-96368000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:96365400-96368400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:96365400-96383800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr13:96365400-96383800	Weak transcription	Thymus	Thymus
36	chr13:96365600-96367800	Enhancers	HMEC	breast
37	chr13:96365600-96375800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr13:96365600-96384600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr13:96365800-96367800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr13:96365800-96367800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr13:96365800-96382600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr13:96365800-96383000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:96365800-96385200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr13:96366000-96367800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr13:96366000-96371600	Strong transcription	Dnd41	blood
46	chr13:96366000-96377600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:96366000-96378200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:96366000-96382200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr13:96366200-96368600	Weak transcription	Ovary	ovary
50	chr13:96366200-96368800	Weak transcription	Fetal Thymus	thymus

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