Variant report

Variant	rs1708624
Chromosome Location	chr17:17157128-17157129
allele	G/T
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	GATA2	chr17:17156917-17157160	SH-SY5Y	brain:	n/a	n/a
2	GATA1	chr17:17156524-17157372	PBDE	blood:	n/a	n/a
3	GATA3	chr17:17156873-17157251	SH-SY5Y	brain:	n/a	chr17:17157066-17157074
4	GATA3	chr17:17156752-17157146	MCF-7	breast:	n/a	chr17:17157066-17157074
5	NR3C1	chr17:17156752-17157167	A549	lung:	n/a	n/a
6	GATA3	chr17:17156863-17157236	T-47D	breast:	n/a	chr17:17157066-17157074

Variant related genes	Relation type
COPS3	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12453455	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600589	0.93[ASN][1000 genomes]
rs12949822	0.81[ASN][1000 genomes]
rs1630656	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708617	0.94[ASN][1000 genomes]
rs1708621	0.94[ASN][1000 genomes]
rs1708628	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736204	1.00[ASN][1000 genomes]
rs1736205	1.00[ASN][1000 genomes]
rs1736208	0.97[ASN][1000 genomes]
rs1736209	0.97[ASN][1000 genomes]
rs1736211	0.94[ASN][1000 genomes]
rs1736212	0.94[ASN][1000 genomes]
rs1736216	0.94[ASN][1000 genomes]
rs1736217	0.94[ASN][1000 genomes]
rs1736221	0.93[ASN][1000 genomes]
rs2012954	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018781	0.94[ASN][1000 genomes]
rs2292527	0.90[ASN][1000 genomes]
rs2472689	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36079048	0.90[ASN][1000 genomes]
rs3866959	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985760	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066065	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62066066	0.86[ASN][1000 genomes]
rs6502564	0.83[ASN][1000 genomes]
rs6502568	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502569	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502570	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502571	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7220577	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221553	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7224598	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225876	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066090	0.94[ASN][1000 genomes]
rs8080386	0.93[ASN][1000 genomes]
rs9892352	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894565	0.94[ASN][1000 genomes]

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	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17141600-17161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:17141800-17162200	Weak transcription	Stomach Mucosa	stomach
3	chr17:17146000-17171000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:17148400-17160000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:17148600-17159000	Strong transcription	Brain Hippocampus Middle	brain
6	chr17:17148600-17161200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:17148600-17167400	Strong transcription	Fetal Intestine Small	intestine
8	chr17:17148600-17172000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr17:17148600-17178800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:17148600-17179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:17148600-17179600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:17148600-17180000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:17148800-17178400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:17148800-17178400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:17148800-17179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:17148800-17179600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:17148800-17179600	Strong transcription	Fetal Muscle Leg	muscle
18	chr17:17148800-17179800	Strong transcription	Fetal Stomach	stomach
19	chr17:17148800-17180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:17148800-17180400	Strong transcription	Fetal Thymus	thymus
21	chr17:17149000-17165200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr17:17149000-17165600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr17:17149000-17165600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:17149000-17165600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:17149000-17165800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:17149000-17165800	Strong transcription	Fetal Brain Female	brain
27	chr17:17149000-17166000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:17149000-17174800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:17149000-17174800	Strong transcription	Adipose Nuclei	Adipose
30	chr17:17149000-17174800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:17149000-17178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:17149000-17178800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr17:17149000-17179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr17:17149000-17179400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:17149000-17180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr17:17149000-17181200	Strong transcription	Dnd41	blood
37	chr17:17149200-17157600	Strong transcription	Brain Substantia Nigra	brain
38	chr17:17149200-17157800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr17:17149200-17157800	Strong transcription	NHEK	skin
40	chr17:17149200-17159400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:17149200-17160400	Strong transcription	Lung	lung
42	chr17:17149200-17164000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:17149200-17164000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr17:17149200-17171400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:17149200-17177400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr17:17149200-17179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:17149200-17179600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr17:17149200-17179600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:17149200-17179800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr17:17149400-17159000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links