Variant report

Variant	rs6736475
Chromosome Location	chr2:98611412-98611413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98523325..98524831-chr2:98610615..98613167,2	MCF-7	breast:
2	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168658	Chromatin interaction
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11892146	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	1.00[AMR][1000 genomes]
rs11898394	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs1503201	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	1.00[AMR][1000 genomes]
rs17022289	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	1.00[AMR][1000 genomes]
rs17025339	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35774346	0.82[AFR][1000 genomes]
rs57434542	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60828800	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	1.00[AMR][1000 genomes]
rs6737992	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	1.00[YRI][hapmap]
rs6746457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	1.00[AMR][1000 genomes]
rs72942856	1.00[AMR][1000 genomes]
rs72942862	1.00[AMR][1000 genomes]
rs72942871	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942876	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942894	0.82[AFR][1000 genomes]
rs72942896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.90[AFR][1000 genomes]
rs72944825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	1.00[AMR][1000 genomes]
rs72946417	1.00[AMR][1000 genomes]
rs72946421	1.00[AMR][1000 genomes]
rs72946425	1.00[AMR][1000 genomes]
rs72946431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	1.00[AMR][1000 genomes]
rs72946448	1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][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	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98600200-98611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:98608200-98611600	Weak transcription	Spleen	Spleen
3	chr2:98608600-98612800	Active TSS	GM12878-XiMat	blood
4	chr2:98609200-98613400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:98609400-98613000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:98609400-98613200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:98609800-98611600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:98609800-98612000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr2:98609800-98612800	Active TSS	NHLF	lung
10	chr2:98609800-98613200	Active TSS	Aorta	Aorta
11	chr2:98609800-98613400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:98610000-98612800	Active TSS	Fetal Muscle Trunk	muscle
13	chr2:98610000-98613000	Active TSS	Fetal Intestine Small	intestine
14	chr2:98610000-98613000	Active TSS	Fetal Stomach	stomach
15	chr2:98610000-98613200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:98610200-98612800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:98610200-98612800	Active TSS	Fetal Intestine Large	intestine
18	chr2:98610200-98613200	Active TSS	Colonic Mucosa	Colon
19	chr2:98610400-98611600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:98610400-98611600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:98610400-98611600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr2:98610400-98611800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:98610400-98613000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:98610400-98613200	Active TSS	Stomach Mucosa	stomach
25	chr2:98610400-98613400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:98610400-98613400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:98610400-98613400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:98610600-98611800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr2:98610600-98611800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:98610600-98611800	Active TSS	Right Atrium	heart
31	chr2:98610600-98612800	Active TSS	Pancreas	Pancrea
32	chr2:98610600-98612800	Active TSS	Right Ventricle	heart
33	chr2:98610600-98612800	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:98610600-98612800	Active TSS	HMEC	breast
35	chr2:98610600-98612800	Active TSS	HSMM	muscle
36	chr2:98610600-98613000	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr2:98610600-98613000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:98610600-98613200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:98610600-98613200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:98610600-98613200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:98610600-98613200	Active TSS	Fetal Kidney	kidney
42	chr2:98610600-98613200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr2:98610600-98613200	Active TSS	Fetal Lung	lung
44	chr2:98610600-98613200	Active TSS	Left Ventricle	heart
45	chr2:98610600-98613200	Active TSS	Ovary	ovary
46	chr2:98610600-98613200	Active TSS	A549	lung
47	chr2:98610600-98613200	Active TSS	HSMMtube	muscle
48	chr2:98610800-98611600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:98610800-98612800	Active TSS	Primary B cells from peripheral blood	blood
50	chr2:98610800-98612800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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