Variant report

Variant	rs3844178
Chromosome Location	chr4:143406833-143406834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143366881..143368916-chr4:143406603..143409121,2	MCF-7	breast:
2	chr4:143406582..143409502-chr4:143418900..143421549,4	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10008498	0.86[AMR][1000 genomes]
rs10011782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12108640	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391099	0.92[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes]
rs1425531	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1425533	1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1425536	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1425537	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1489581	0.92[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs1593360	0.94[JPT][hapmap]
rs17016163	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs17016175	0.92[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs17016233	0.89[JPT][hapmap]
rs17016306	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1817970	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs1834391	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113996	0.94[EUR][1000 genomes]
rs2113997	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2322795	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2874841	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2874865	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28822497	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3863128	0.90[AMR][1000 genomes]
rs3913163	0.92[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3913164	0.84[CHD][hapmap]
rs4956444	0.86[AMR][1000 genomes]
rs4975308	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60924405	0.94[EUR][1000 genomes]
rs6837163	0.89[JPT][hapmap]
rs713071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672965	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs9308151	0.84[AMR][1000 genomes]
rs976564	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs979511	0.83[MEX][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143369200-143410600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143397400-143414800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143401800-143418600	Weak transcription	Fetal Heart	heart
4	chr4:143405800-143407200	Enhancers	Primary T cells from cord blood	blood
5	chr4:143406000-143407000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr4:143406000-143407200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:143406000-143407400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:143406200-143407200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:143406200-143407400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:143406200-143407400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:143406200-143407400	Enhancers	Fetal Intestine Small	intestine
12	chr4:143406400-143407200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr4:143406400-143407200	Enhancers	Fetal Intestine Large	intestine
14	chr4:143406400-143407400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:143406400-143407600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr4:143406800-143407000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:143406800-143407200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:143406800-143407400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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