Variant report

Variant	rs59355797
Chromosome Location	chr1:173943311-173943312
allele	C/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	CTCF	chr1:173943302-173943416	MCF-7	breast:	n/a	n/a
2	CTCF	chr1:173943301-173943415	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:173943300-173943450	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr1:173943240-173943390	HMEC	breast:	n/a	n/a
5	CTCF	chr1:173943260-173943410	HCM	heart:	n/a	n/a
6	CTCF	chr1:173943292-173943420	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:173943240-173943390	GM12872	blood:	n/a	n/a
8	CTCF	chr1:173943299-173943414	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:173943289-173943431	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:173943260-173943410	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173941961..173943858-chr1:173944447..173947260,2	K562	blood:

Variant related genes	Relation type
RNA5SP68	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1322769	1.00[AMR][1000 genomes]
rs16846397	1.00[AMR][1000 genomes]
rs16846483	1.00[AMR][1000 genomes]
rs2227620	1.00[AMR][1000 genomes]
rs57006357	1.00[AMR][1000 genomes]
rs57343517	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57664780	1.00[AMR][1000 genomes]
rs58576036	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58735809	1.00[AMR][1000 genomes]
rs58930477	1.00[AMR][1000 genomes]
rs59846661	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667627	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6704413	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025612	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025620	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027407	1.00[AMR][1000 genomes]
rs73027443	1.00[AMR][1000 genomes]
rs73027460	1.00[AMR][1000 genomes]
rs73027463	1.00[AMR][1000 genomes]
rs73027464	1.00[AMR][1000 genomes]
rs73027488	1.00[AMR][1000 genomes]
rs73035134	1.00[AMR][1000 genomes]
rs73035139	1.00[AMR][1000 genomes]
rs73037076	1.00[AMR][1000 genomes]
rs73037083	1.00[AMR][1000 genomes]
rs73037097	1.00[AMR][1000 genomes]
rs73041050	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73041059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7519571	1.00[AMR][1000 genomes]
rs7531236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547873	1.00[AMR][1000 genomes]
rs9726181	1.00[AMR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active 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	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
5	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking 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	27 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	chr1:173899800-173953800	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr1:173900000-173958600	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:173901600-173966400	Strong transcription	Dnd41	blood
12	chr1:173902200-173954600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:173902600-173954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:173904800-173954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:173905200-173954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:173906800-173959000	Strong transcription	Liver	Liver
20	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:173910400-173952200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
23	chr1:173922200-173954000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:173923400-173954400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:173923800-173953800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:173923800-173954400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:173923800-173955600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:173927600-173954200	Strong transcription	Placenta	Placenta
30	chr1:173928800-173953800	Strong transcription	Fetal Intestine Large	intestine
31	chr1:173929000-173962200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:173929600-173952800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:173931000-173946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:173931200-173944000	Strong transcription	HUVEC	blood vessel
35	chr1:173931200-173946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:173931200-173949800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
40	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:173931800-173946000	Weak transcription	Esophagus	oesophagus
42	chr1:173931800-173946200	Weak transcription	Right Ventricle	heart
43	chr1:173931800-173948400	Weak transcription	Spleen	Spleen
44	chr1:173931800-173950800	Weak transcription	Pancreas	Pancrea
45	chr1:173932200-173954000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:173932800-173944600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:173932800-173946400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr1:173932800-173951200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:173933200-173954600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:173933400-173947000	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links