Variant report

Variant	rs6005861
Chromosome Location	chr22:29154237-29154238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29135896..29138704-chr22:29152370..29155070,2	MCF-7	breast:
2	chr22:29137252..29140773-chr22:29152307..29154305,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10427858	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165475	0.82[YRI][hapmap]
rs12166716	1.00[YRI][hapmap]
rs12167378	0.82[YRI][hapmap]
rs12330071	0.93[EUR][1000 genomes]
rs17878936	0.89[LWK][hapmap];0.82[YRI][hapmap]
rs2073326	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs2206061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228260	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28448648	0.84[EUR][1000 genomes]
rs41281603	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56119508	1.00[EUR][1000 genomes]
rs5752839	0.88[MEX][hapmap]
rs5762893	0.88[MEX][hapmap]
rs5762900	0.88[MEX][hapmap]
rs5762906	0.88[MEX][hapmap]
rs5997389	0.89[AFR][1000 genomes]
rs5997390	0.89[AFR][1000 genomes]
rs5997391	0.90[JPT][hapmap];0.86[MEX][hapmap]
rs5997401	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005856	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6005870	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005874	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005898	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005899	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60116790	0.97[AFR][1000 genomes]
rs7288513	0.88[MEX][hapmap]
rs7290364	0.88[MEX][hapmap]
rs73388803	0.89[AFR][1000 genomes]
rs9306460	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9620817	0.81[JPT][hapmap]
rs9620826	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9620828	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9620833	0.89[AFR][1000 genomes]
rs9620839	1.00[YRI][hapmap]
rs9625544	0.82[YRI][hapmap]
rs9625547	0.80[AFR][1000 genomes]
rs9625548	0.94[AFR][1000 genomes]
rs9625551	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9625554	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9625558	0.84[EUR][1000 genomes]
rs9625562	0.81[AFR][1000 genomes]
rs9625565	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625568	0.97[AFR][1000 genomes]
rs9625572	0.97[AFR][1000 genomes]
rs9625575	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9625580	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625645	0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs9625657	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv516312	chr22:29153759-29160314	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29139400-29156400	Weak transcription	Stomach Mucosa	stomach
2	chr22:29139800-29156000	Weak transcription	HMEC	breast
3	chr22:29140800-29155800	Weak transcription	Fetal Brain Female	brain
4	chr22:29141200-29156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29143400-29156600	Weak transcription	Brain Substantia Nigra	brain
6	chr22:29143600-29155600	Weak transcription	Gastric	stomach
7	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:29143800-29155600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr22:29143800-29156000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr22:29143800-29156400	Weak transcription	Brain Angular Gyrus	brain
11	chr22:29144400-29156200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr22:29144400-29156200	Weak transcription	Brain Hippocampus Middle	brain
13	chr22:29144400-29156200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr22:29144600-29155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr22:29144600-29155800	Weak transcription	Brain Germinal Matrix	brain
16	chr22:29144800-29154600	Weak transcription	Right Atrium	heart
17	chr22:29145200-29154800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr22:29145400-29154800	Weak transcription	Left Ventricle	heart
19	chr22:29145400-29155400	Weak transcription	Colon Smooth Muscle	Colon
20	chr22:29145400-29157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr22:29145600-29155400	Weak transcription	HSMM	muscle
22	chr22:29145600-29155600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr22:29145600-29155600	Weak transcription	HSMMtube	muscle
24	chr22:29145800-29155800	Weak transcription	Ovary	ovary
25	chr22:29145800-29156200	Weak transcription	Spleen	Spleen
26	chr22:29145800-29156600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr22:29146000-29155400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr22:29146000-29155400	Weak transcription	HepG2	liver
30	chr22:29146000-29155600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr22:29146000-29155600	Weak transcription	Colonic Mucosa	Colon
32	chr22:29146000-29155800	Weak transcription	Brain Anterior Caudate	brain
33	chr22:29146000-29155800	Weak transcription	GM12878-XiMat	blood
34	chr22:29146000-29156400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr22:29146000-29156600	Weak transcription	Adipose Nuclei	Adipose
36	chr22:29146600-29156200	Weak transcription	Primary B cells from cord blood	blood
37	chr22:29146800-29156600	Weak transcription	Primary T cells from cord blood	blood
38	chr22:29146800-29156600	Weak transcription	Fetal Intestine Large	intestine
39	chr22:29147200-29155800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr22:29147400-29155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:29147400-29156000	Weak transcription	Hela-S3	cervix
42	chr22:29147400-29156200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr22:29147600-29155600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr22:29147800-29155600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:29147800-29155600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr22:29147800-29155800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:29147800-29156400	Weak transcription	Lung	lung
48	chr22:29148000-29155800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr22:29148000-29164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr22:29148000-29167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links