Variant report

Variant	rs6662839
Chromosome Location	chr1:165722646-165722647
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	chr1:165720854..165729861-chr1:165736355..165740477,8	K562	blood:
2	chr1:165722333..165726093-chr1:165736872..165739220,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224358	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10800153	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.94[EUR][1000 genomes]
rs12133745	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691499	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790049	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814471	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.80[EUR][1000 genomes]
rs4233408	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.82[AMR][1000 genomes]
rs6660601	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.86[EUR][1000 genomes]
rs6696454	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165705000-165724800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:165710400-165727000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:165712400-165726800	Weak transcription	Fetal Lung	lung
8	chr1:165712400-165727000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:165712400-165727200	Weak transcription	HMEC	breast
10	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
11	chr1:165713000-165722800	Weak transcription	GM12878-XiMat	blood
12	chr1:165713400-165733600	Weak transcription	NHEK	skin
13	chr1:165713600-165722800	Weak transcription	Fetal Kidney	kidney
14	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:165716800-165728000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:165717000-165724000	Strong transcription	Osteobl	bone
17	chr1:165717400-165724200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:165717400-165728000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:165718000-165725800	Weak transcription	HSMM	muscle
20	chr1:165718400-165725000	Weak transcription	Primary B cells from cord blood	blood
21	chr1:165718800-165725600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:165719400-165723600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:165719600-165725000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:165720000-165725600	Strong transcription	Dnd41	blood
25	chr1:165720200-165723600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:165720200-165725600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:165720800-165733400	Weak transcription	A549	lung
28	chr1:165721400-165723400	Strong transcription	Fetal Brain Female	brain
29	chr1:165721400-165725000	Strong transcription	NHLF	lung
30	chr1:165721600-165723800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:165721800-165722800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:165721800-165722800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:165721800-165722800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:165721800-165723000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:165721800-165723000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:165721800-165723000	Strong transcription	Gastric	stomach
37	chr1:165721800-165723000	Strong transcription	Lung	lung
38	chr1:165721800-165723000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:165721800-165723000	Strong transcription	Thymus	Thymus
40	chr1:165721800-165723000	Strong transcription	Spleen	Spleen
41	chr1:165721800-165723200	Strong transcription	Colon Smooth Muscle	Colon
42	chr1:165721800-165723400	Strong transcription	Fetal Stomach	stomach
43	chr1:165721800-165723600	Strong transcription	Ovary	ovary
44	chr1:165721800-165723600	Strong transcription	K562	blood
45	chr1:165721800-165724000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:165721800-165724000	Weak transcription	Primary T cells from cord blood	blood
47	chr1:165721800-165724000	Strong transcription	Placenta	Placenta
48	chr1:165721800-165724200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:165721800-165724200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:165721800-165724200	Strong transcription	Liver	Liver

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