Variant report

Variant	rs9620828
Chromosome Location	chr22:29185674-29185675
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29145305..29148162-chr22:29185055..29187826,2	K562	blood:
2	chr22:29136633..29138535-chr22:29184332..29186376,2	MCF-7	breast:
3	chr22:29151815..29154169-chr22:29184646..29186865,2	MCF-7	breast:
4	chr22:29171571..29173553-chr22:29184100..29185761,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10222265	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10427858	0.92[AFR][1000 genomes]
rs11913747	1.00[AMR][1000 genomes]
rs12165475	0.87[YRI][hapmap]
rs12165715	1.00[CHB][hapmap]
rs12165893	1.00[CHB][hapmap]
rs12166245	1.00[CHB][hapmap]
rs12166716	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12167378	0.87[YRI][hapmap]
rs12168765	1.00[CHB][hapmap]
rs12169262	1.00[CHB][hapmap]
rs12169460	1.00[CHB][hapmap]
rs13057011	1.00[CHB][hapmap]
rs16986649	1.00[AMR][1000 genomes]
rs17878936	0.82[YRI][hapmap]
rs17882700	1.00[AMR][1000 genomes]
rs2073326	0.82[YRI][hapmap]
rs2206061	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs59060951	1.00[ASN][1000 genomes]
rs5997389	0.87[AFR][1000 genomes]
rs5997390	0.87[AFR][1000 genomes]
rs5997401	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs59974795	1.00[ASN][1000 genomes]
rs6005822	1.00[AMR][1000 genomes]
rs6005824	1.00[AMR][1000 genomes]
rs6005856	0.87[AFR][1000 genomes]
rs6005861	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6005870	0.97[AFR][1000 genomes]
rs6005898	0.97[AFR][1000 genomes]
rs60116790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61339566	1.00[AMR][1000 genomes]
rs7286816	1.00[ASN][1000 genomes]
rs7289534	1.00[CHB][hapmap]
rs7293232	1.00[CHB][hapmap]
rs73388803	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73388808	1.00[ASN][1000 genomes]
rs9620808	1.00[CHB][hapmap]
rs9620810	1.00[CHB][hapmap]
rs9620811	1.00[CHB][hapmap]
rs9620826	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9620833	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9620839	1.00[YRI][hapmap]
rs9625512	1.00[CHB][hapmap]
rs9625513	1.00[CHB][hapmap]
rs9625514	1.00[CHB][hapmap]
rs9625520	1.00[CHB][hapmap]
rs9625521	1.00[CHB][hapmap]
rs9625523	1.00[CHB][hapmap]
rs9625524	1.00[CHB][hapmap]
rs9625544	0.87[YRI][hapmap]
rs9625547	0.83[AFR][1000 genomes]
rs9625548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625554	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625565	0.97[AFR][1000 genomes]
rs9625568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625580	0.97[AFR][1000 genomes]
rs9625586	1.00[ASN][1000 genomes]
rs9625602	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625603	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625645	0.85[YRI][hapmap]

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	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	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
3	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
3	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29171200-29188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:29171400-29186000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:29171800-29186200	Strong transcription	Fetal Thymus	thymus
11	chr22:29172400-29186200	Strong transcription	Placenta	Placenta
12	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
13	chr22:29175000-29186000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr22:29175600-29185800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr22:29175800-29186200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr22:29176400-29186000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr22:29176800-29190200	Weak transcription	Hela-S3	cervix
18	chr22:29180400-29186200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr22:29180400-29191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:29180600-29186000	Strong transcription	Fetal Lung	lung
21	chr22:29180600-29191000	Weak transcription	Small Intestine	intestine
22	chr22:29180800-29189800	Weak transcription	HMEC	breast
23	chr22:29180800-29190200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr22:29181200-29186000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr22:29181600-29191000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr22:29181800-29186400	Strong transcription	Fetal Intestine Large	intestine
27	chr22:29182000-29188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:29182000-29191000	Weak transcription	Fetal Brain Male	brain
29	chr22:29182200-29186200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr22:29182200-29188600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr22:29182200-29188600	Weak transcription	Lung	lung
32	chr22:29182400-29185800	Weak transcription	Fetal Stomach	stomach
33	chr22:29182400-29190000	Weak transcription	Stomach Mucosa	stomach
34	chr22:29182400-29190000	Weak transcription	HSMMtube	muscle
35	chr22:29182400-29190000	Weak transcription	NHEK	skin
36	chr22:29182400-29190200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr22:29182400-29190800	Weak transcription	Gastric	stomach
38	chr22:29182400-29191200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr22:29182600-29186200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr22:29182600-29189800	Weak transcription	NHLF	lung
41	chr22:29182600-29190200	Weak transcription	A549	lung
42	chr22:29182600-29190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:29182600-29191000	Weak transcription	Ovary	ovary
44	chr22:29182600-29191200	Weak transcription	Esophagus	oesophagus
45	chr22:29182800-29190000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr22:29182800-29190000	Weak transcription	Right Ventricle	heart
47	chr22:29182800-29190400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr22:29183000-29186800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr22:29183000-29190000	Weak transcription	Brain Anterior Caudate	brain
50	chr22:29183000-29190000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links