Variant report

Variant	rs1610602
Chromosome Location	chr6:29702061-29702062
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29702012..29703555-chr6:29719487..29721197,2	K562	blood:

Variant related genes	Relation type
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1419696	0.88[ASN][1000 genomes]
rs1610601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610608	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610612	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610615	0.96[AFR][1000 genomes]
rs1610617	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1610621	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1610625	0.94[ASN][1000 genomes]
rs1610629	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610633	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1610729	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1610735	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1611284	0.83[ASN][1000 genomes]
rs1622223	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1628578	0.88[ASN][1000 genomes]
rs1632957	0.85[ASN][1000 genomes]
rs1633063	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1633065	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1633088	0.94[ASN][1000 genomes]
rs1633096	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633098	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633099	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633106	0.88[ASN][1000 genomes]
rs1633107	0.88[ASN][1000 genomes]
rs1736915	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737077	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248927	0.89[ASN][1000 genomes]
rs2517910	0.94[CHD][hapmap];0.86[JPT][hapmap]
rs2517911	0.80[ASN][1000 genomes]
rs2517942	0.88[ASN][1000 genomes]
rs2517945	0.86[ASN][1000 genomes]
rs2523392	0.89[ASN][1000 genomes]
rs2523394	0.89[ASN][1000 genomes]
rs2523398	0.86[ASN][1000 genomes]
rs2523399	0.89[ASN][1000 genomes]
rs2523400	0.89[ASN][1000 genomes]
rs2735054	0.89[ASN][1000 genomes]
rs2735055	0.89[ASN][1000 genomes]
rs2844847	0.88[ASN][1000 genomes]
rs885941	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs885942	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885943	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885944	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885945	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs885946	0.85[ASN][1000 genomes]
rs929158	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929159	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929160	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
9	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1610602	BTN3A3	cis	parietal	SCAN
rs1610602	HIST1H3I	cis	cerebellum	SCAN
rs1610602	HLA-A	cis	lymphoblastoid	GTEx
rs1610602	SLC17A3	cis	parietal	SCAN
rs1610602	ZNF323	cis	parietal	SCAN
rs1610602	HIST1H2BB	cis	cerebellum	SCAN
rs1610602	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1610602	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1610602	ZKSCAN3	cis	parietal	SCAN
rs1610602	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:29692800-29712000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:29693200-29711400	Weak transcription	Pancreas	Pancrea
5	chr6:29693400-29715600	Weak transcription	Esophagus	oesophagus
6	chr6:29693600-29715600	Weak transcription	NHLF	lung
7	chr6:29693800-29705400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:29693800-29715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
10	chr6:29694000-29707000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:29694000-29711200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:29694000-29711400	Weak transcription	Gastric	stomach
13	chr6:29694000-29712200	Weak transcription	Aorta	Aorta
14	chr6:29694000-29715600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:29694200-29705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:29696000-29702200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:29696000-29705600	Weak transcription	Right Ventricle	heart
18	chr6:29696000-29715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:29696000-29715600	Weak transcription	Ovary	ovary
20	chr6:29696200-29702200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:29696200-29703800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:29696200-29703800	Weak transcription	Left Ventricle	heart
23	chr6:29696200-29705600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:29696200-29705800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:29696200-29711800	Weak transcription	Adipose Nuclei	Adipose
26	chr6:29696200-29715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:29696200-29715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:29696200-29715600	Weak transcription	Liver	Liver
29	chr6:29696400-29702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:29696400-29710800	Weak transcription	Lung	lung
31	chr6:29696400-29711400	Weak transcription	Spleen	Spleen
32	chr6:29696400-29711800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:29696400-29712000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:29696400-29715400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:29696600-29702200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:29696600-29702200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:29696600-29715600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:29696800-29702400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:29696800-29714600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
41	chr6:29699000-29702600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:29699200-29712400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:29699400-29702400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:29699800-29702400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:29700000-29715200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:29700600-29711600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:29701800-29702200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:29701800-29702200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:29701800-29702400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:29701800-29702400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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