Variant report

Variant	rs16872758
Chromosome Location	chr4:22509525-22509526
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:22507819..22511270-chr4:22511320..22514443,4	MCF-7	breast:
2	chr4:22508358..22510140-chr4:22512148..22515141,2	MCF-7	breast:
3	chr4:22508191..22514199-chr4:22515176..22519559,12	MCF-7	breast:
4	chr4:22505951..22512123-chr4:22514706..22518696,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11728370	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11730156	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs11731725	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872759	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2086010	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2100886	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58855874	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61793423	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6818597	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs73114174	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73114193	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73114194	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7675740	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs7685164	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22488600-22516000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:22497000-22515600	Weak transcription	Fetal Stomach	stomach
3	chr4:22500400-22510600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:22500400-22510600	Enhancers	HMEC	breast
5	chr4:22500600-22510800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:22502200-22515600	Weak transcription	Primary T cells from cord blood	blood
7	chr4:22502800-22509800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:22502800-22515600	Weak transcription	Fetal Kidney	kidney
9	chr4:22503200-22515600	Weak transcription	NHDF-Ad	bronchial
10	chr4:22504000-22514200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:22504800-22510800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:22504800-22512200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:22504800-22513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:22504800-22514200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:22505000-22515200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:22505200-22512200	Weak transcription	Fetal Intestine Large	intestine
17	chr4:22505400-22509800	Weak transcription	Hela-S3	cervix
18	chr4:22505400-22511800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:22505400-22515400	Weak transcription	A549	lung
20	chr4:22505600-22510400	Enhancers	Liver	Liver
21	chr4:22505600-22513200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:22505600-22515600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:22506000-22510800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr4:22506200-22510800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:22506400-22511800	Weak transcription	Left Ventricle	heart
26	chr4:22506400-22513800	Weak transcription	Brain Germinal Matrix	brain
27	chr4:22506600-22511800	Weak transcription	Esophagus	oesophagus
28	chr4:22506600-22515800	Weak transcription	Aorta	Aorta
29	chr4:22506800-22510200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:22506800-22511800	Weak transcription	Right Ventricle	heart
31	chr4:22507000-22510200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:22507000-22515200	Weak transcription	HSMM	muscle
33	chr4:22507200-22510600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:22507400-22515400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:22507600-22509800	Enhancers	Fetal Heart	heart
36	chr4:22507600-22510600	Enhancers	HepG2	liver
37	chr4:22507600-22516200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:22508000-22509800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:22508000-22514400	Weak transcription	Ovary	ovary
40	chr4:22508000-22516200	Weak transcription	Small Intestine	intestine
41	chr4:22508200-22513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:22508400-22509600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:22508400-22509600	Enhancers	Rectal Smooth Muscle	rectum
44	chr4:22508400-22510200	Weak transcription	Lung	lung
45	chr4:22508400-22516000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:22508600-22515800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:22508800-22510400	Enhancers	Colon Smooth Muscle	Colon
48	chr4:22508800-22510800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:22508800-22510800	Enhancers	Psoas Muscle	Psoas
50	chr4:22509000-22509600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links