Variant report

Variant	rs9625640
Chromosome Location	chr22:29299209-29299210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29298276..29299796-chr22:29305846..29307998,2	MCF-7	breast:
2	chr22:29294042..29296336-chr22:29297392..29300176,2	MCF-7	breast:
3	chr22:29195884..29197508-chr22:29298766..29301210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16986814	1.00[EUR][1000 genomes]
rs2881637	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752820	0.87[EUR][1000 genomes]
rs5752830	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752839	0.85[EUR][1000 genomes]
rs5762873	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762876	1.00[ASN][1000 genomes]
rs5762890	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762891	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762893	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762895	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762900	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762906	0.85[EUR][1000 genomes]
rs5762907	0.87[EUR][1000 genomes]
rs7286026	0.87[EUR][1000 genomes]
rs7288513	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7290364	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73388860	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8137589	0.90[EUR][1000 genomes]
rs9306461	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625613	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625621	1.00[EUR][1000 genomes]
rs9625622	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625628	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625641	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9625645	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625647	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29288000-29301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29291200-29300600	Weak transcription	Psoas Muscle	Psoas
3	chr22:29292400-29300600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:29293000-29299800	Weak transcription	A549	lung
5	chr22:29295600-29299800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr22:29295600-29299800	Weak transcription	NHDF-Ad	bronchial
7	chr22:29295600-29300600	Weak transcription	Brain Substantia Nigra	brain
8	chr22:29295800-29300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr22:29296200-29299400	Weak transcription	NH-A	brain
10	chr22:29296200-29300400	Weak transcription	HSMMtube	muscle
11	chr22:29296400-29300400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr22:29296600-29300000	Weak transcription	Osteobl	bone
13	chr22:29296600-29300400	Weak transcription	HSMM	muscle
14	chr22:29296800-29299800	Weak transcription	Fetal Brain Female	brain
15	chr22:29296800-29310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:29297400-29300600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr22:29298200-29299800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr22:29298200-29301000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:29298400-29299400	Genic enhancers	Fetal Intestine Small	intestine
20	chr22:29298400-29301200	Enhancers	Adipose Nuclei	Adipose
21	chr22:29298400-29301200	Enhancers	Fetal Muscle Leg	muscle
22	chr22:29298400-29301400	Enhancers	Right Ventricle	heart
23	chr22:29298400-29302800	Enhancers	Liver	Liver
24	chr22:29298400-29308400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr22:29298400-29310400	Enhancers	Fetal Intestine Large	intestine
26	chr22:29298600-29299600	Enhancers	Colon Smooth Muscle	Colon
27	chr22:29298600-29299800	Enhancers	NHEK	skin
28	chr22:29298600-29300000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr22:29298600-29300200	Genic enhancers	HepG2	liver
30	chr22:29298600-29300200	Enhancers	HMEC	breast
31	chr22:29298600-29300800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr22:29298600-29300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr22:29298600-29300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr22:29298600-29301000	Enhancers	Duodenum Mucosa	Duodenum
35	chr22:29298600-29301200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr22:29298600-29302000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr22:29298600-29302400	Enhancers	Placenta	Placenta
38	chr22:29298600-29302600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:29298600-29302600	Enhancers	Fetal Lung	lung
40	chr22:29298600-29302800	Enhancers	Fetal Kidney	kidney
41	chr22:29298600-29304600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr22:29298600-29305000	Enhancers	Brain Anterior Caudate	brain
43	chr22:29298600-29305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:29298800-29300000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr22:29298800-29300000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:29298800-29300000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr22:29298800-29301000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:29298800-29301200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:29298800-29301200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:29298800-29301200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links