Variant report

Variant	rs17397129
Chromosome Location	chr1:10345462-10345463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10287445..10289464-chr1:10344922..10346758,2	K562	blood:

Variant related genes	Relation type
ENSG00000264881	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10864454	0.89[EUR][1000 genomes]
rs11121542	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121548	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120465	0.87[EUR][1000 genomes]
rs12120499	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125492	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135774	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12137527	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139158	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142043	0.88[EUR][1000 genomes]
rs17396340	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400878	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401588	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762289	0.88[EUR][1000 genomes]
rs4240912	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4240913	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4846204	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846214	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846217	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs58036267	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61383940	0.84[EUR][1000 genomes]
rs6670157	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6679596	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6693965	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694081	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6702280	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703602	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525661	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs997482	1.00[CEU][hapmap];0.84[EUR][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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv545382	chr1:10309026-10377221	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10312800-10347200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:10314200-10356400	Weak transcription	Small Intestine	intestine
4	chr1:10314200-10363400	Weak transcription	Fetal Brain Male	brain
5	chr1:10314800-10347000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:10315000-10355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:10315400-10373400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:10316800-10380200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:10317400-10355200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:10317400-10356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:10317600-10355600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:10318400-10367600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:10320600-10363000	Weak transcription	Gastric	stomach
14	chr1:10321400-10359000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:10321800-10353200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:10322400-10356400	Weak transcription	Esophagus	oesophagus
17	chr1:10322800-10363200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:10324200-10356200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:10324400-10356400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:10326000-10352000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:10327200-10352400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:10328400-10347000	Weak transcription	Aorta	Aorta
23	chr1:10331600-10368000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:10331800-10356400	Weak transcription	Fetal Thymus	thymus
25	chr1:10332200-10363800	Weak transcription	Thymus	Thymus
26	chr1:10333200-10359200	Weak transcription	Stomach Mucosa	stomach
27	chr1:10334400-10360000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:10334600-10347200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:10335000-10360000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:10335200-10352000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:10335400-10347400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:10335600-10349400	Strong transcription	Brain Germinal Matrix	brain
33	chr1:10335600-10359000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:10335800-10359000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:10337000-10349400	Strong transcription	Fetal Intestine Large	intestine
36	chr1:10337600-10347000	Weak transcription	Pancreas	Pancrea
37	chr1:10338200-10348800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:10339400-10350600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:10339400-10352400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:10339400-10355600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:10340000-10354600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:10340000-10356600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:10340600-10347400	Strong transcription	HepG2	liver
44	chr1:10340600-10350200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:10340800-10346800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:10341000-10346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:10341000-10347000	Weak transcription	Psoas Muscle	Psoas
48	chr1:10341200-10348200	Strong transcription	Adipose Nuclei	Adipose
49	chr1:10341600-10346000	Strong transcription	HSMM	muscle
50	chr1:10341800-10345600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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