Variant report

Variant	rs3805251
Chromosome Location	chr4:144295952-144295953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:144295930-144296135	T-47D	breast:	n/a	n/a
2	EP300	chr4:144295923-144296300	T-47D	breast:	n/a	n/a
3	FOXA1	chr4:144295948-144296176	T-47D	breast:	n/a	n/a
4	FOXA1	chr4:144295896-144296136	T-47D	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:144289833..144292177-chr4:144294492..144296058,2	K562	blood:
2	chr4:144292852..144297100-chr4:144298409..144302941,5	K562	blood:
3	chr4:144256664..144258280-chr4:144293930..144296084,2	MCF-7	breast:
4	chr4:144289833..144291469-chr4:144294402..144296058,2	K562	blood:
5	chr4:144290996..144292995-chr4:144295055..144297084,2	MCF-7	breast:
6	chr4:144295435..144296093-chr5:75459165..75460000,2	MCF-7	breast:
7	chr4:144279254..144282177-chr4:144295139..144296728,2	MCF-7	breast:

No data

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000109458	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10013047	0.98[ASN][1000 genomes]
rs1027851	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1027852	0.98[ASN][1000 genomes]
rs10519691	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs11100786	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11100787	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11100788	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11100789	0.83[ASN][1000 genomes]
rs11730569	0.97[ASN][1000 genomes]
rs11945731	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12647531	0.97[ASN][1000 genomes]
rs12649592	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13123498	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs1397526	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1397527	0.80[CHD][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1397528	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1472873	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1510879	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1510880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866756	0.98[ASN][1000 genomes]
rs2048408	0.96[ASN][1000 genomes]
rs2055730	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2119270	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2196908	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2196909	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs300890	0.82[JPT][hapmap]
rs300893	0.82[JPT][hapmap]
rs300894	0.82[JPT][hapmap]
rs300895	0.82[JPT][hapmap]
rs300904	0.82[JPT][hapmap]
rs300905	0.82[JPT][hapmap]
rs300910	0.89[ASN][1000 genomes]
rs300911	0.80[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300912	0.80[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300913	0.88[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300914	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300915	0.88[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs300916	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs300917	0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs300918	0.81[ASN][1000 genomes]
rs300919	0.82[JPT][hapmap]
rs34095331	0.87[ASN][1000 genomes]
rs34439737	0.90[ASN][1000 genomes]
rs3792652	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs3792653	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792655	0.97[ASN][1000 genomes]
rs3805238	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3805245	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805246	0.97[ASN][1000 genomes]
rs3805247	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs3805249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3805252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805254	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3805256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805257	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3828512	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828513	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3828514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55758499	0.97[ASN][1000 genomes]
rs55894236	0.97[ASN][1000 genomes]
rs6537154	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs719392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679870	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7680959	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs906571	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018566	chr4:144284927-144298930	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	nsv437941	chr4:144285683-144295952	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv1021714	chr4:144288438-144299191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv1033347	chr4:144288438-144299563	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 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	chr4:144272800-144299800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:144277400-144296800	Weak transcription	HSMMtube	muscle
3	chr4:144281200-144296800	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:144281400-144296800	Weak transcription	Fetal Kidney	kidney
5	chr4:144283000-144302200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:144284000-144296600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:144284000-144296600	Weak transcription	Fetal Thymus	thymus
8	chr4:144284400-144299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:144286000-144298200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:144288200-144296600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:144291000-144299800	Weak transcription	Pancreas	Pancrea
12	chr4:144291400-144296600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:144291400-144296600	Weak transcription	Fetal Lung	lung
14	chr4:144291600-144296200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:144291600-144296200	Weak transcription	Lung	lung
16	chr4:144291600-144296600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:144291600-144296600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:144291600-144296600	Weak transcription	Right Atrium	heart
19	chr4:144291600-144296800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:144291600-144299400	Weak transcription	Fetal Intestine Large	intestine
21	chr4:144291800-144302200	Weak transcription	Esophagus	oesophagus
22	chr4:144293200-144296600	Enhancers	Colon Smooth Muscle	Colon
23	chr4:144293200-144298000	Enhancers	Fetal Heart	heart
24	chr4:144293200-144299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:144293200-144299800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:144293200-144302400	Enhancers	Brain Substantia Nigra	brain
27	chr4:144293400-144298200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr4:144293600-144296600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:144293600-144302000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:144293800-144296400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:144293800-144296600	Weak transcription	HMEC	breast
32	chr4:144294000-144296000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:144294000-144296200	Weak transcription	Stomach Mucosa	stomach
34	chr4:144294000-144302200	Weak transcription	Spleen	Spleen
35	chr4:144294000-144302400	Weak transcription	Gastric	stomach
36	chr4:144294200-144296600	Weak transcription	GM12878-XiMat	blood
37	chr4:144294400-144296000	Enhancers	Right Ventricle	heart
38	chr4:144294400-144296600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:144294400-144297400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:144294800-144297200	Enhancers	Ovary	ovary
41	chr4:144295000-144296000	Weak transcription	Left Ventricle	heart
42	chr4:144295000-144296200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:144295000-144296200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:144295000-144302800	Enhancers	Brain Cingulate Gyrus	brain
45	chr4:144295200-144296000	Enhancers	Brain Hippocampus Middle	brain
46	chr4:144295200-144297400	Enhancers	K562	blood
47	chr4:144295200-144298200	Enhancers	Primary B cells from cord blood	blood
48	chr4:144295200-144301000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:144295200-144302400	Enhancers	Brain Anterior Caudate	brain
50	chr4:144295400-144296000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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