Variant report

Variant	rs13302653
Chromosome Location	chr9:21833046-21833047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:21832214..21835164-chr9:21835316..21836950,2	MCF-7	breast:
2	chr9:21830900..21838533-chr9:22079723..22086252,27	MCF-7	breast:
3	chr9:21830834..21834057-chr9:21834525..21838075,6	MCF-7	breast:
4	chr9:21831674..21838507-chr9:22079741..22086703,33	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10118757	0.85[JPT][hapmap]
rs10217131	0.85[CEU][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs10217379	0.83[CEU][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs10511700	0.93[JPT][hapmap]
rs10811631	0.93[JPT][hapmap]
rs10965157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10965158	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12004745	0.92[JPT][hapmap]
rs12337510	0.91[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2039971	0.92[JPT][hapmap]
rs2282245	0.83[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3802393	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs3931609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295749	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4375086	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs4399022	0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4543632	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs6475581	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs6475583	0.85[CEU][hapmap];0.93[JPT][hapmap]
rs6475584	0.91[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6475588	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6475589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7026112	0.84[AMR][1000 genomes]
rs7029287	0.92[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7033148	0.84[EUR][1000 genomes]
rs7041509	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7042302	0.84[AMR][1000 genomes]
rs7042728	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7851125	0.91[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs7859886	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7860126	0.91[CEU][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7867176	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7869680	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7871477	0.91[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7874112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885518	0.91[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
4	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:21816400-21836600	Weak transcription	Psoas Muscle	Psoas
7	chr9:21816600-21833800	Weak transcription	Fetal Brain Male	brain
8	chr9:21816800-21833200	Weak transcription	Brain Angular Gyrus	brain
9	chr9:21817400-21837800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:21817800-21840600	Weak transcription	Colonic Mucosa	Colon
11	chr9:21818600-21840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:21818800-21840400	Weak transcription	Right Ventricle	heart
13	chr9:21819400-21833800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:21819400-21840400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:21819400-21841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:21823800-21840400	Strong transcription	Fetal Muscle Leg	muscle
17	chr9:21824200-21840400	Strong transcription	Fetal Lung	lung
18	chr9:21825000-21840000	Strong transcription	Fetal Intestine Large	intestine
19	chr9:21825000-21840600	Strong transcription	Dnd41	blood
20	chr9:21825000-21841800	Strong transcription	Primary T cells from cord blood	blood
21	chr9:21825000-21841800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr9:21825200-21836600	Strong transcription	Fetal Stomach	stomach
23	chr9:21825200-21840200	Weak transcription	Pancreas	Pancrea
24	chr9:21825200-21840800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:21825200-21841400	Strong transcription	Fetal Thymus	thymus
26	chr9:21825200-21842200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:21825400-21833800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:21825400-21834200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:21825400-21834400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:21825400-21840400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:21825400-21840600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr9:21825600-21833200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:21825600-21833200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:21825800-21834000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:21825800-21838600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:21825800-21840200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:21825800-21840600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:21825800-21840600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:21826000-21833600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:21826000-21838400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:21826000-21840800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:21826400-21833800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:21827200-21834400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr9:21827800-21834200	Weak transcription	Esophagus	oesophagus
45	chr9:21828200-21838200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:21828200-21838800	Strong transcription	Fetal Intestine Small	intestine
47	chr9:21828400-21837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:21828800-21836000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:21828800-21836800	Genic enhancers	NHEK	skin
50	chr9:21829200-21834200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links