Variant report

Variant	rs17617250
Chromosome Location	chr17:46010893-46010894
allele	A/C
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	POLR2A	chr17:46010288-46011140	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45973395..45975502-chr17:46008931..46011121,2	MCF-7	breast:
2	chr17:45977677..45979429-chr17:46010688..46013383,2	MCF-7	breast:
3	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:
4	chr17:46010778..46013733-chr5:72250921..72253254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266601	TF binding region
ENSG00000264019	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000157107	Chromatin interaction
ENSG00000272081	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11079804	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108833	0.89[CHB][hapmap]
rs11545723	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11654010	0.81[CHB][hapmap]
rs12602494	0.83[CHB][hapmap]
rs12948368	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476578	0.87[CHB][hapmap]
rs1476579	0.87[CHB][hapmap]
rs2525087	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2525088	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2525090	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2525093	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2525096	0.87[CHB][hapmap]
rs2525098	0.87[CHB][hapmap]
rs2597171	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2597172	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2597173	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2597174	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2597179	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2875746	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2905851	0.87[CHB][hapmap]
rs2905852	0.88[CHB][hapmap]
rs3096	0.81[CHB][hapmap]
rs34428844	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35004787	0.87[AMR][1000 genomes]
rs35132293	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35480192	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35533494	0.87[AMR][1000 genomes]
rs35702577	0.83[AMR][1000 genomes]
rs4793693	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4793733	0.83[CHB][hapmap]
rs4793734	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4794225	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56119022	0.87[AMR][1000 genomes]
rs62067368	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66721410	0.87[AMR][1000 genomes]
rs7211859	0.88[CHB][hapmap]
rs729785	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs729786	0.88[CHB][hapmap]
rs737130	0.88[CHB][hapmap]
rs739853	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7503584	0.87[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
2	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
3	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
4	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
5	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr17:46002400-46013400	Weak transcription	Stomach Mucosa	stomach
9	chr17:46003000-46012200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:46003200-46012000	Weak transcription	HMEC	breast
11	chr17:46003200-46012000	Weak transcription	NHDF-Ad	bronchial
12	chr17:46003200-46012200	Weak transcription	NH-A	brain
13	chr17:46003200-46012200	Weak transcription	NHEK	skin
14	chr17:46003200-46014200	Weak transcription	GM12878-XiMat	blood
15	chr17:46003200-46018400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:46004400-46012600	Weak transcription	Hela-S3	cervix
17	chr17:46004600-46013200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:46004600-46018200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:46005400-46012400	Weak transcription	NHLF	lung
20	chr17:46005400-46017400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:46005400-46018200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:46006200-46017800	Weak transcription	Small Intestine	intestine
23	chr17:46006600-46011200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:46006600-46013400	Weak transcription	Right Atrium	heart
25	chr17:46006800-46011000	Strong transcription	Fetal Stomach	stomach
26	chr17:46006800-46015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:46007000-46011200	Strong transcription	Fetal Intestine Small	intestine
28	chr17:46007000-46012000	Weak transcription	HSMM	muscle
29	chr17:46007000-46012200	Weak transcription	Osteobl	bone
30	chr17:46007000-46015600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:46007000-46018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:46007000-46018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr17:46007200-46018200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr17:46007600-46012200	Weak transcription	HSMMtube	muscle
35	chr17:46007600-46013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:46007600-46017400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:46007600-46018200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:46007600-46018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:46007800-46018200	Weak transcription	Colonic Mucosa	Colon
40	chr17:46007800-46018400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:46007800-46018800	Weak transcription	Gastric	stomach
42	chr17:46008000-46012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:46008000-46013200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:46008000-46013200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr17:46008000-46015400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:46008000-46015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:46008000-46015400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:46008000-46015600	Weak transcription	Adipose Nuclei	Adipose
49	chr17:46008000-46015800	Weak transcription	Brain Hippocampus Middle	brain
50	chr17:46008000-46018200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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