Variant report

Variant	rs2797516
Chromosome Location	chr9:5799489-5799490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5798897..5800040-chr9:5885951..5886842,5	MCF-7	breast:
2	chr9:5799205..5801900-chr9:5831455..5833894,2	MCF-7	breast:
3	chr9:5799071..5800155-chr9:5899057..5900015,4	MCF-7	breast:
4	chr9:5798939..5799987-chr9:5899066..5899993,6	MCF-7	breast:
5	chr9:5799337..5799887-chr9:6054224..6055029,2	K562	blood:

Variant related genes	Relation type
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10975340	1.00[EUR][1000 genomes]
rs1141025	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260128	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260130	0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260132	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260134	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260135	1.00[EUR][1000 genomes]
rs1745887	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1745888	0.92[AFR][1000 genomes]
rs1776008	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2476262	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2760408	1.00[EUR][1000 genomes]
rs2760409	0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2760410	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2797512	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2797514	1.00[EUR][1000 genomes]
rs2797517	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2797519	1.00[EUR][1000 genomes]
rs58370080	1.00[EUR][1000 genomes]
rs6477001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477002	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7037680	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7038243	0.90[YRI][hapmap]
rs7042100	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046793	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73377834	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1019444	chr9:5598677-5807009	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5779200-5809600	Weak transcription	NHDF-Ad	bronchial
2	chr9:5779200-5832200	Weak transcription	Fetal Brain Male	brain
3	chr9:5779600-5814000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:5779600-5827800	Weak transcription	Small Intestine	intestine
5	chr9:5784200-5831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:5786800-5832200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:5787000-5830200	Weak transcription	Dnd41	blood
8	chr9:5787200-5804200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:5787200-5815000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:5787400-5801000	Weak transcription	Colonic Mucosa	Colon
11	chr9:5787400-5832000	Weak transcription	Fetal Brain Female	brain
12	chr9:5787600-5801000	Weak transcription	Fetal Intestine Large	intestine
13	chr9:5787600-5801000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:5787600-5801600	Weak transcription	Thymus	Thymus
15	chr9:5787600-5806400	Weak transcription	Fetal Stomach	stomach
16	chr9:5787600-5809400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:5787600-5809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:5787600-5809600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:5787600-5809600	Weak transcription	Left Ventricle	heart
20	chr9:5787600-5812400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:5787600-5812800	Weak transcription	Lung	lung
22	chr9:5787600-5817600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:5787600-5831600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:5787600-5832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:5787600-5832200	Weak transcription	Esophagus	oesophagus
26	chr9:5787800-5801200	Weak transcription	Stomach Mucosa	stomach
27	chr9:5787800-5818000	Weak transcription	HSMM	muscle
28	chr9:5788000-5809600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:5788000-5817600	Weak transcription	K562	blood
30	chr9:5789800-5802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:5789800-5825200	Weak transcription	Gastric	stomach
32	chr9:5790000-5824000	Weak transcription	Pancreas	Pancrea
33	chr9:5790600-5808200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:5791400-5809400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:5791600-5809400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:5791800-5809600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:5791800-5809600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:5792000-5814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:5792200-5809400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:5792400-5805600	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:5792800-5800200	Weak transcription	HMEC	breast
42	chr9:5794000-5808400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr9:5794600-5821800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:5794600-5825600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:5795000-5809800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:5795200-5809600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:5795200-5809800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:5796000-5799600	Strong transcription	HepG2	liver
49	chr9:5796200-5799800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr9:5797000-5800800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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