Variant report

Variant	rs343482
Chromosome Location	chr9:6024347-6024348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6007035..6009287-chr9:6023689..6025799,2	K562	blood:
2	chr9:6015628..6017411-chr9:6023313..6026226,2	MCF-7	breast:
3	chr9:6013606..6016921-chr9:6022468..6025086,4	MCF-7	breast:
4	chr9:6024216..6024722-chr9:6049502..6050057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183354	Chromatin interaction
ENSG00000263575	Chromatin interaction
ENSG00000137040	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733517	1.00[CEU][hapmap]
rs10733518	0.90[EUR][1000 genomes]
rs10733520	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10739079	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10758731	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs1418740	1.00[CEU][hapmap]
rs1478940	0.80[ASN][1000 genomes]
rs16923578	1.00[CEU][hapmap]
rs186913	1.00[CEU][hapmap]
rs2150703	1.00[CEU][hapmap]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs2773340	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2773341	1.00[EUR][1000 genomes]
rs343469	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs343471	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs343480	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs343483	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs343500	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs3739649	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs404267	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs419595	0.90[EUR][1000 genomes]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs451361	0.92[ASN][1000 genomes]
rs457313	0.81[ASN][1000 genomes]
rs459718	0.90[EUR][1000 genomes]
rs460564	1.00[EUR][1000 genomes]
rs4740833	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs4742131	1.00[CEU][hapmap]
rs56705560	0.84[ASN][1000 genomes]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap]
rs7026454	0.84[YRI][hapmap]
rs7029833	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs7034210	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7039265	0.81[ASN][1000 genomes]
rs7042947	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7044750	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs7846916	1.00[EUR][1000 genomes]
rs7866793	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7868062	1.00[CEU][hapmap]
rs899381	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6023200-6029800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:6024000-6024400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr9:6024000-6024400	Enhancers	Primary B cells from peripheral blood	blood
4	chr9:6024000-6024400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:6024000-6024400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:6024000-6024400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:6024000-6024400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:6024000-6024400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:6024000-6024400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:6024000-6024400	Active TSS	Duodenum Mucosa	Duodenum
11	chr9:6024000-6024400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:6024000-6024400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr9:6024000-6024400	Enhancers	Stomach Mucosa	stomach
14	chr9:6024000-6024400	Flanking Active TSS	HepG2	liver
15	chr9:6024000-6024400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr9:6024000-6024400	Active TSS	Osteobl	bone
17	chr9:6024000-6024600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr9:6024000-6024600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr9:6024000-6024800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:6024000-6025200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:6024000-6025400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:6024200-6024400	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr9:6024200-6024400	Enhancers	Aorta	Aorta
24	chr9:6024200-6024400	Active TSS	A549	lung
25	chr9:6024200-6024400	Enhancers	Dnd41	blood
26	chr9:6024200-6024400	Flanking Active TSS	Hela-S3	cervix
27	chr9:6024200-6024400	Bivalent/Poised TSS	HUVEC	blood vessel
28	chr9:6024200-6024400	Active TSS	NHEK	skin
29	chr9:6024200-6024600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr9:6024200-6024600	Enhancers	GM12878-XiMat	blood
31	chr9:6024200-6024800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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