Variant report

Variant	rs2235370
Chromosome Location	chr1:209946027-209946028
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	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
3	POLR2A	chr1:209945732-209947149	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
5	STAT5A	chr1:209942515-209946308	GM12878	blood:	n/a	chr1:209942981-209942989 chr1:209942982-209942994 chr1:209945841-209945853 chr1:209943537-209943545

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209945724..209947520-chr1:209953789..209956019,2	K562	blood:

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10489343	0.85[AMR][1000 genomes]
rs10779514	0.81[AMR][1000 genomes]
rs10779515	0.85[AMR][1000 genomes]
rs10863789	0.85[AMR][1000 genomes]
rs10863790	0.85[AMR][1000 genomes]
rs1109430	0.81[AMR][1000 genomes]
rs11119345	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119347	0.85[AMR][1000 genomes]
rs11119348	0.85[AMR][1000 genomes]
rs12058100	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12075674	0.81[AMR][1000 genomes]
rs12080691	0.81[AMR][1000 genomes]
rs12081405	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12083685	0.88[ASN][1000 genomes]
rs12405750	0.85[AMR][1000 genomes]
rs12561766	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12566152	0.85[AMR][1000 genomes]
rs17015076	1.00[EUR][1000 genomes]
rs17015078	1.00[EUR][1000 genomes]
rs17015217	0.94[AMR][1000 genomes]
rs17015255	0.85[AMR][1000 genomes]
rs17015268	0.85[AMR][1000 genomes]
rs1856161	0.94[AMR][1000 genomes]
rs2038053	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076149	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076151	0.88[AMR][1000 genomes]
rs2142860	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235371	0.94[AMR][1000 genomes]
rs2235377	0.85[AMR][1000 genomes]
rs2236902	1.00[EUR][1000 genomes]
rs2272866	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2282740	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2294406	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2298930	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3753517	0.85[AMR][1000 genomes]
rs41274836	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4140636	0.89[ASN][1000 genomes]
rs4329516	0.81[AMR][1000 genomes]
rs4545339	1.00[EUR][1000 genomes]
rs4844491	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844494	0.94[AMR][1000 genomes]
rs4844893	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844894	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56822893	0.85[EUR][1000 genomes]
rs57283682	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788672	0.83[EUR][1000 genomes]
rs7515014	1.00[EUR][1000 genomes]
rs7517461	1.00[EUR][1000 genomes]
rs7528642	1.00[EUR][1000 genomes]
rs7532021	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3429215	chr1:209942329-209947327	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3449118	chr1:209942529-209946727	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3393757	chr1:209943129-209946427	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	esv3391985	chr1:209943579-209946077	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
2	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
3	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209943200-209950600	Weak transcription	Psoas Muscle	Psoas
5	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:209943600-209951000	Weak transcription	HSMMtube	muscle
7	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:209943800-209950800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:209943800-209954600	Weak transcription	NHEK	skin
10	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:209944000-209946200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:209944000-209952800	Weak transcription	HMEC	breast
16	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:209944200-209946400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
19	chr1:209944400-209947200	Weak transcription	Right Atrium	heart
20	chr1:209944400-209948800	Genic enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:209944600-209946400	Genic enhancers	Thymus	Thymus
22	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:209944800-209946200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
24	chr1:209944800-209947800	Genic enhancers	Primary B cells from cord blood	blood
25	chr1:209944800-209950000	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr1:209944800-209951200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:209944800-209956600	Weak transcription	Right Ventricle	heart
30	chr1:209945000-209946200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:209945000-209946400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
32	chr1:209945000-209946600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:209945000-209947200	Weak transcription	Dnd41	blood
34	chr1:209945000-209950200	Weak transcription	Fetal Intestine Large	intestine
35	chr1:209945000-209953400	Weak transcription	Liver	Liver
36	chr1:209945000-209953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:209945000-209953800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:209945000-209956000	Weak transcription	Brain Anterior Caudate	brain
39	chr1:209945000-209956400	Weak transcription	Left Ventricle	heart
40	chr1:209945000-209956600	Weak transcription	Adipose Nuclei	Adipose
41	chr1:209945000-209956600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:209945000-209956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:209945000-209956600	Weak transcription	Esophagus	oesophagus
44	chr1:209945000-209956600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:209945000-209956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:209945000-209956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:209945200-209949000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:209945200-209954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:209945200-209956600	Weak transcription	Colonic Mucosa	Colon
50	chr1:209945200-209956600	Weak transcription	Pancreas	Pancrea

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