Variant report

Variant	rs3806144
Chromosome Location	chr6:16742118-16742119
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	chr6:16740481..16745919-chr6:16759194..16763421,5	MCF-7	breast:
2	chr6:16731670..16733382-chr6:16740577..16742802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229931	Chromatin interaction
ENSG00000124788	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434861	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10456788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10456789	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10456790	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10456791	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10949379	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12194640	0.86[CEU][hapmap]
rs16878970	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16879003	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459484	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6915772	0.95[EUR][1000 genomes]
rs9350015	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

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	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16706400-16742600	Weak transcription	Pancreas	Pancrea
2	chr6:16713800-16747800	Weak transcription	Brain Germinal Matrix	brain
3	chr6:16720200-16747800	Weak transcription	Fetal Brain Male	brain
4	chr6:16728800-16744400	Weak transcription	Lung	lung
5	chr6:16729200-16742600	Weak transcription	Gastric	stomach
6	chr6:16731600-16746000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:16732000-16745600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:16732200-16746800	Weak transcription	Hela-S3	cervix
9	chr6:16732200-16754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:16732400-16744400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:16732600-16748000	Weak transcription	Colonic Mucosa	Colon
12	chr6:16736800-16742600	Enhancers	HMEC	breast
13	chr6:16736800-16742800	Enhancers	Colon Smooth Muscle	Colon
14	chr6:16736800-16748800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr6:16737400-16747400	Weak transcription	Fetal Brain Female	brain
16	chr6:16737600-16746600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:16737600-16747600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:16737600-16759400	Weak transcription	Thymus	Thymus
19	chr6:16737800-16742600	Enhancers	NHEK	skin
20	chr6:16738000-16742400	Weak transcription	Fetal Thymus	thymus
21	chr6:16738000-16743000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:16738000-16749800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:16738200-16745600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:16738400-16742200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:16738400-16745800	Weak transcription	Liver	Liver
26	chr6:16738600-16742600	Weak transcription	Small Intestine	intestine
27	chr6:16738600-16744400	Weak transcription	Aorta	Aorta
28	chr6:16738600-16745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:16738600-16745800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:16739000-16752200	Weak transcription	HUVEC	blood vessel
31	chr6:16739800-16745600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:16739800-16748000	Weak transcription	Adipose Nuclei	Adipose
33	chr6:16740000-16747400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:16740200-16742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:16740200-16742400	Weak transcription	Placenta	Placenta
36	chr6:16740200-16742400	Weak transcription	Fetal Stomach	stomach
37	chr6:16740200-16742400	Weak transcription	Left Ventricle	heart
38	chr6:16740200-16742400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr6:16740200-16742400	Weak transcription	Spleen	Spleen
40	chr6:16740200-16742600	Enhancers	Fetal Intestine Small	intestine
41	chr6:16740200-16742800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:16740200-16742800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:16740200-16743200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:16740200-16743800	Weak transcription	Esophagus	oesophagus
45	chr6:16740200-16743800	Weak transcription	Right Atrium	heart
46	chr6:16740200-16744000	Enhancers	HSMM	muscle
47	chr6:16740200-16744800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:16740200-16744800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:16740200-16748000	Weak transcription	Right Ventricle	heart
50	chr6:16740400-16742400	Weak transcription	Fetal Muscle Trunk	muscle

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