Variant report

Variant	rs975229
Chromosome Location	chr4:16199117-16199118
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	chr4:16026644..16029440-chr4:16198521..16200680,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1373109	0.86[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1443368	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443369	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443370	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712479	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17479949	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2011754	0.94[EUR][1000 genomes]
rs28377010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485928	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496446	0.92[EUR][1000 genomes]
rs28726676	0.94[EUR][1000 genomes]
rs317858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs317859	0.84[AFR][1000 genomes]
rs317860	0.91[AFR][1000 genomes]
rs317867	0.91[AFR][1000 genomes]
rs35046072	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35367114	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798874	0.92[EUR][1000 genomes]
rs73798875	0.92[EUR][1000 genomes]
rs73798883	0.89[EUR][1000 genomes]
rs7690701	0.92[EUR][1000 genomes]
rs961450	0.92[EUR][1000 genomes];1.00[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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
6	chr4:16184200-16200600	Strong transcription	Fetal Thymus	thymus
7	chr4:16187400-16199600	Weak transcription	Hela-S3	cervix
8	chr4:16191400-16207000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:16192200-16204800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:16193000-16205000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:16193000-16207600	Weak transcription	Brain Germinal Matrix	brain
12	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
13	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
14	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
15	chr4:16193200-16205800	Weak transcription	Fetal Intestine Small	intestine
16	chr4:16193200-16206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:16193200-16207000	Weak transcription	Pancreas	Pancrea
18	chr4:16193200-16208000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:16193200-16208000	Weak transcription	Lung	lung
20	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
21	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
22	chr4:16193600-16203000	Weak transcription	HepG2	liver
23	chr4:16193600-16208600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:16193800-16206400	Weak transcription	K562	blood
25	chr4:16194200-16202400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:16195000-16204800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:16195400-16199600	Weak transcription	Right Ventricle	heart
28	chr4:16195400-16199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:16195400-16199600	Weak transcription	Small Intestine	intestine
30	chr4:16195400-16201400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:16195400-16201400	Weak transcription	Left Ventricle	heart
32	chr4:16195400-16201600	Weak transcription	Thymus	Thymus
33	chr4:16195400-16203200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr4:16195400-16207000	Weak transcription	Gastric	stomach
35	chr4:16196200-16201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:16196200-16203400	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:16196200-16207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:16197200-16199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:16197400-16200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:16197600-16199200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:16197800-16199200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:16197800-16199200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:16197800-16199200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr4:16197800-16200400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr4:16197800-16200400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr4:16197800-16200600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr4:16197800-16200800	Enhancers	Stomach Mucosa	stomach
48	chr4:16198000-16199200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:16198000-16199600	Enhancers	Liver	Liver
50	chr4:16198000-16200000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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