Variant report

Variant	rs2523399
Chromosome Location	chr6:29700079-29700080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29692291..29694908-chr6:29698271..29700498,2	K562	blood:

Variant related genes	Relation type
ENSG00000204642	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1610601	0.88[ASN][1000 genomes]
rs1610602	0.89[ASN][1000 genomes]
rs1610608	0.87[ASN][1000 genomes]
rs1610612	0.89[ASN][1000 genomes]
rs1610617	0.86[ASN][1000 genomes]
rs1610621	0.87[ASN][1000 genomes]
rs1610625	0.84[ASN][1000 genomes]
rs1610629	0.83[ASN][1000 genomes]
rs1610633	0.84[ASN][1000 genomes]
rs1610729	0.84[ASN][1000 genomes]
rs1610735	0.85[ASN][1000 genomes]
rs1611284	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1633063	0.85[ASN][1000 genomes]
rs1633065	0.84[ASN][1000 genomes]
rs1633088	0.84[ASN][1000 genomes]
rs1633096	0.89[ASN][1000 genomes]
rs1633098	0.89[ASN][1000 genomes]
rs1633099	0.89[ASN][1000 genomes]
rs1736915	0.89[ASN][1000 genomes]
rs1737077	0.85[ASN][1000 genomes]
rs2248927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517910	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2517942	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517945	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523392	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523394	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844847	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885942	0.89[ASN][1000 genomes]
rs885943	0.89[ASN][1000 genomes]
rs885944	0.89[ASN][1000 genomes]
rs885945	0.82[ASN][1000 genomes]
rs929158	0.89[ASN][1000 genomes]
rs929159	0.89[ASN][1000 genomes]
rs929160	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv462673	chr6:29689590-29700183	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv601230	chr6:29689590-29700183	Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv883531	chr6:29692562-29705402	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2523399	HLA-G	cis	multi-tissue	Pritchard
rs2523399	HLA-A	cis	multi-tissue	Pritchard
rs2523399	ZFP57	cis	multi-tissue	Pritchard
rs2523399	TPD52L2	trans	multi-tissue	Pritchard
rs2523399	TFG	trans	multi-tissue	Pritchard
rs2523399	HLA-A	trans	brain	seeQTL
rs2523399	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2523399	HLA-H	cis	multi-tissue	Pritchard
rs2523399	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs2523399	HLA-A	cis	brain	seeQTL
rs2523399	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2523399	NDUFS1	trans	multi-tissue	Pritchard
rs2523399	KIT	trans	multi-tissue	Pritchard
rs2523399	HLA.A29.1	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29701800	Weak transcription	HMEC	breast
2	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
6	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
7	chr6:29693600-29715600	Weak transcription	NHLF	lung
8	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
11	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:29694000-29711400	Weak transcription	Gastric	stomach
14	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
15	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:29694200-29701800	Weak transcription	NHEK	skin
17	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:29696000-29702200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:29696000-29705600	Weak transcription	Right Ventricle	heart
20	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:29696000-29715600	Weak transcription	Ovary	ovary
22	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:29696200-29701800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:29696200-29702200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:29696200-29703800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:29696200-29703800	Weak transcription	Left Ventricle	heart
27	chr6:29696200-29705600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:29696200-29705800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:29696200-29715600	Weak transcription	Liver	Liver
33	chr6:29696400-29701800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:29696400-29701800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:29696400-29702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:29696400-29710800	Weak transcription	Lung	lung
37	chr6:29696400-29711400	Weak transcription	Spleen	Spleen
38	chr6:29696400-29711800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:29696400-29712000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:29696600-29700600	Weak transcription	Primary B cells from cord blood	blood
42	chr6:29696600-29702200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:29696600-29702200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:29696600-29715600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:29696800-29702000	Weak transcription	GM12878-XiMat	blood
46	chr6:29696800-29702400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:29696800-29714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
49	chr6:29699000-29702600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:29699200-29712400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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