Variant report

Variant	rs12529288
Chromosome Location	chr6:31058975-31058976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30881108..30884685-chr6:31055628..31059015,3	K562	blood:
2	chr6:30688777..30690812-chr6:31058826..31061400,2	K562	blood:
3	chr6:31055515..31057079-chr6:31058653..31060271,2	K562	blood:
4	chr6:30881781..30883446-chr6:31057515..31059055,2	K562	blood:

Variant related genes	Relation type
ENSG00000196230	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10947134	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10947135	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10947137	0.82[AMR][1000 genomes]
rs12527394	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12662091	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2233963	0.92[AMR][1000 genomes]
rs2233970	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2233972	0.96[AMR][1000 genomes]
rs2233973	0.84[ASN][1000 genomes]
rs2233983	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2233984	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2233985	0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2517473	0.85[ASN][1000 genomes]
rs2894179	0.97[ASN][1000 genomes]
rs34209658	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35802713	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734854	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4495304	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713431	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947246	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4947296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947297	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4947299	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4947302	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9263460	0.95[ASN][1000 genomes]
rs9263477	0.95[ASN][1000 genomes]
rs9263499	0.98[ASN][1000 genomes]
rs9263512	0.97[ASN][1000 genomes]
rs9263572	0.96[ASN][1000 genomes]
rs9263578	0.96[ASN][1000 genomes]
rs9295949	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295950	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348854	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357108	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378152	0.85[AMR][1000 genomes]
rs9380215	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380217	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9391708	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9391709	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9394037	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404978	0.89[AFR][1000 genomes]
rs9405049	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31040600-31062400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:31051000-31062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:31052000-31061000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:31055200-31059000	Weak transcription	K562	blood
5	chr6:31055200-31059400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:31055200-31060600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:31055200-31060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:31055200-31062000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:31055200-31062200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:31055400-31059800	Weak transcription	A549	lung
11	chr6:31055400-31060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:31055400-31061000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:31055400-31061000	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:31055400-31062400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:31055600-31060600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:31055800-31059400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:31055800-31059400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:31055800-31060600	Weak transcription	HUVEC	blood vessel
19	chr6:31055800-31061000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr6:31055800-31061000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:31055800-31061800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:31058400-31061400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:31058600-31059200	Enhancers	Stomach Mucosa	stomach
24	chr6:31058600-31059400	Enhancers	HepG2	liver
25	chr6:31058800-31060200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr6:31058800-31062000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:31058800-31066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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