Variant report

Variant	rs7042947
Chromosome Location	chr9:5898109-5898110
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5894386..5896231-chr9:5898006..5899746,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10733517	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733518	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733520	1.00[CEU][hapmap]
rs10739079	1.00[CEU][hapmap]
rs10758731	1.00[CEU][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap]
rs10815301	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10815302	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap]
rs1342853	0.84[ASN][1000 genomes]
rs1418740	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16923578	1.00[CEU][hapmap]
rs186913	1.00[CEU][hapmap]
rs2150703	1.00[CEU][hapmap]
rs2225469	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs2773340	0.90[EUR][1000 genomes]
rs2773341	0.90[EUR][1000 genomes]
rs343469	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs343471	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs343480	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs343482	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs343483	0.90[EUR][1000 genomes]
rs343500	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs3739649	1.00[CEU][hapmap]
rs404267	0.90[EUR][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs419595	0.81[EUR][1000 genomes]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap]
rs459718	0.81[EUR][1000 genomes]
rs460564	0.90[EUR][1000 genomes]
rs4740833	1.00[CEU][hapmap]
rs4742131	1.00[CEU][hapmap]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7029833	1.00[CEU][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039787	0.81[EUR][1000 genomes]
rs7044750	1.00[CEU][hapmap]
rs7846916	0.86[CHB][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]
rs899381	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1033546	chr9:5875201-5900427	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
2	chr9:5859000-5906600	Weak transcription	Ovary	ovary
3	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
4	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:5871200-5898400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:5883000-5906400	Weak transcription	Fetal Brain Male	brain
7	chr9:5884600-5910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:5885800-5898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:5886800-5905000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:5886800-5920400	Weak transcription	GM12878-XiMat	blood
11	chr9:5886800-5920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:5886800-5922000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:5887000-5921600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:5889000-5898400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:5892600-5921600	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:5893000-5900200	Weak transcription	Fetal Kidney	kidney
17	chr9:5893000-5920000	Weak transcription	Thymus	Thymus
18	chr9:5893200-5908200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:5893400-5899400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:5893400-5900400	Weak transcription	HSMM	muscle
21	chr9:5894000-5910400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:5894200-5899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:5894400-5905200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:5894400-5920400	Weak transcription	NH-A	brain
25	chr9:5894600-5910400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:5894600-5919800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:5895000-5898400	Weak transcription	Liver	Liver
28	chr9:5895000-5898600	Weak transcription	Fetal Intestine Large	intestine
29	chr9:5895000-5899600	Weak transcription	A549	lung
30	chr9:5895000-5908600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:5895400-5899400	Strong transcription	Fetal Stomach	stomach
32	chr9:5895400-5899800	Strong transcription	Primary T cells from cord blood	blood
33	chr9:5895400-5904000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:5895600-5898200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:5895600-5899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:5895600-5899600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr9:5895800-5899000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:5895800-5899800	Strong transcription	Adipose Nuclei	Adipose
39	chr9:5895800-5910400	Weak transcription	NHDF-Ad	bronchial
40	chr9:5896000-5899400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:5896000-5899800	Strong transcription	Fetal Muscle Leg	muscle
42	chr9:5896000-5921600	Weak transcription	Lung	lung
43	chr9:5896200-5899200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:5896200-5899200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:5896200-5920200	Weak transcription	Psoas Muscle	Psoas
46	chr9:5896200-5920800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:5896200-5921200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:5896400-5898400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:5896400-5899000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:5896400-5899400	Strong transcription	Left Ventricle	heart

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