Variant report

Variant	rs10190872
Chromosome Location	chr2:128273072-128273073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr2:128272967-128273296	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128268468..128273715-chr2:128281746..128285691,7	MCF-7	breast:
2	chr2:128271646..128276478-chr2:128281725..128284912,6	MCF-7	breast:
3	chr2:128268614..128270650-chr2:128272810..128274940,2	MCF-7	breast:
4	chr2:128272088..128276196-chr2:128278536..128286742,8	K562	blood:
5	chr2:128271568..128276709-chr2:128278536..128286742,13	K562	blood:

No data

Variant related genes	Relation type
IWS1	TF binding region
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10206221	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12475217	0.89[ASN][1000 genomes]
rs12621149	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13397441	0.86[ASN][1000 genomes]
rs13399231	0.93[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs13415053	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1549767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17015347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17015399	0.85[ASN][1000 genomes]
rs173013	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17522960	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2078028	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2176595	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2249646	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2566564	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2679402	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2679407	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs334139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs334140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334142	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334153	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334155	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4423553	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4662582	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs55981410	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56217122	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56234754	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58462277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59934067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61342606	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6707186	0.83[ASN][1000 genomes]
rs6707425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6713317	0.87[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs6722447	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6727506	0.81[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs6731270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748999	0.81[TSI][hapmap]
rs6757654	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72958594	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72958600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570609	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.86[ASN][1000 genomes]
rs7572181	0.86[ASN][1000 genomes]
rs7574209	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7574215	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7576217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7598346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7603777	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777547	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777549	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777551	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs777558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs777559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs777561	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs777562	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs777563	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10190872	DDX43	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
3	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128263400-128275400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:128266000-128282800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:128267200-128274400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr2:128267200-128282000	Weak transcription	Fetal Brain Male	brain
8	chr2:128267400-128273200	Strong transcription	Primary B cells from cord blood	blood
9	chr2:128267600-128281200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:128267600-128282000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:128267800-128275000	Strong transcription	GM12878-XiMat	blood
12	chr2:128267800-128276200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:128268400-128275400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:128268400-128275600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:128268400-128281600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:128268600-128273600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:128268600-128281600	Strong transcription	Fetal Thymus	thymus
18	chr2:128269200-128274600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:128269600-128274400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:128270000-128274000	Enhancers	Fetal Heart	heart
21	chr2:128270200-128282600	Weak transcription	Small Intestine	intestine
22	chr2:128270400-128274200	Weak transcription	K562	blood
23	chr2:128270400-128276600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:128270600-128274800	Strong transcription	Dnd41	blood
25	chr2:128271000-128274200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:128271000-128278600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:128271200-128273600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr2:128271200-128274200	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr2:128271400-128273200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr2:128271400-128273400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:128271400-128273400	Strong transcription	Placenta	Placenta
32	chr2:128271400-128274200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:128271400-128274200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr2:128271400-128274200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:128271400-128274200	Enhancers	HSMMtube	muscle
36	chr2:128271400-128274400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:128271400-128274400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:128271400-128274400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:128271400-128274600	Strong transcription	Fetal Stomach	stomach
40	chr2:128271400-128275200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:128271400-128275400	Strong transcription	NHEK	skin
42	chr2:128271400-128281400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:128271400-128281800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:128271400-128281800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr2:128271600-128273200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:128271600-128273600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:128271600-128273600	Strong transcription	Gastric	stomach
48	chr2:128271600-128274200	Strong transcription	Thymus	Thymus
49	chr2:128271600-128274200	Genic enhancers	Spleen	Spleen
50	chr2:128271600-128274400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links