Variant report

Variant	rs9900338
Chromosome Location	chr17:59975939-59975940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:59975800-59975950	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59972585..59974357-chr17:59975555..59977763,3	K562	blood:
2	chr17:59975871..59977661-chr20:55841428..55844280,2	MCF-7	breast:
3	chr17:59972401..59976325-chr17:60003389..60005361,4	MCF-7	breast:
4	chr17:59974815..59976373-chr5:179047439..179050401,2	MCF-7	breast:

Variant related genes	Relation type
INTS2	TF binding region
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2138005	1.00[AMR][1000 genomes]
rs59176712	1.00[AMR][1000 genomes]
rs7213469	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73991950	1.00[AMR][1000 genomes]
rs73991951	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9900745	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9908729	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9913705	1.00[AMR][1000 genomes]
rs9914236	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
3	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
4	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
6	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
7	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
8	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
10	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:59947400-59977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:59948000-59981800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:59948200-59980600	Weak transcription	HMEC	breast
16	chr17:59948200-59986800	Weak transcription	Fetal Kidney	kidney
17	chr17:59950000-59979200	Weak transcription	NHLF	lung
18	chr17:59950800-59981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:59951600-59989600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr17:59952800-59981400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:59953800-59985600	Weak transcription	Small Intestine	intestine
23	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:59954600-59984800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:59955200-59979600	Weak transcription	HSMMtube	muscle
26	chr17:59958000-59987600	Weak transcription	Esophagus	oesophagus
27	chr17:59959000-59996800	Weak transcription	Gastric	stomach
28	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
29	chr17:59962000-59977000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr17:59962400-59979400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:59963400-59989600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:59963800-59989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:59964000-59983200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr17:59964800-59979200	Weak transcription	Hela-S3	cervix
35	chr17:59965000-59977600	Weak transcription	NHEK	skin
36	chr17:59965200-59976600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:59965600-59981400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:59966000-59978000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr17:59966000-59984600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
41	chr17:59966200-59981600	Weak transcription	Thymus	Thymus
42	chr17:59966200-59982400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:59966200-59983000	Weak transcription	Spleen	Spleen
44	chr17:59966200-59987600	Weak transcription	Ovary	ovary
45	chr17:59966200-59998000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr17:59966400-59976800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr17:59967000-59976000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr17:59967600-59977200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr17:59967600-59979800	Weak transcription	Colon Smooth Muscle	Colon
50	chr17:59967600-59980600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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