Variant report

Variant	rs6720537
Chromosome Location	chr2:39668754-39668755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39666476..39669114-chr2:39673200..39674751,2	K562	blood:
2	chr2:39539961..39541586-chr2:39667193..39669640,2	K562	blood:
3	chr2:39663101..39666745-chr2:39668624..39671198,3	MCF-7	breast:
4	chr2:39668408..39675131-chr2:39676739..39679699,8	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169501	0.85[ASN][1000 genomes]
rs10173722	0.84[ASN][1000 genomes]
rs10196447	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10199459	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10199948	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11124683	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896389	0.91[EUR][1000 genomes]
rs12328714	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12624242	0.83[MKK][hapmap]
rs12712640	0.88[MKK][hapmap]
rs17023530	0.94[EUR][1000 genomes]
rs17023542	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17023547	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17023600	0.94[EUR][1000 genomes]
rs17023611	0.94[EUR][1000 genomes]
rs17023684	1.00[EUR][1000 genomes]
rs17023696	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs17023773	0.97[EUR][1000 genomes]
rs17446102	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446515	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446690	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs17505580	0.94[EUR][1000 genomes]
rs17505877	0.94[EUR][1000 genomes]
rs2056653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111383	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373530	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs2373532	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732052	1.00[EUR][1000 genomes]
rs4670273	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55761128	1.00[EUR][1000 genomes]
rs6544227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544229	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720951	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721049	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6721740	0.97[EUR][1000 genomes]
rs6731310	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758596	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924009	1.00[EUR][1000 genomes]
rs7559436	1.00[EUR][1000 genomes]
rs7577097	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7588265	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7596222	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7605939	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39670000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:39665600-39684200	Weak transcription	Lung	lung
5	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
6	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
8	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:39666400-39670600	Weak transcription	Liver	Liver
12	chr2:39666600-39671000	Weak transcription	Right Atrium	heart
13	chr2:39666600-39673000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:39666600-39675800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:39666800-39669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:39666800-39669600	Weak transcription	Fetal Intestine Small	intestine
18	chr2:39666800-39670800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:39666800-39671400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:39666800-39677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:39666800-39681600	Weak transcription	Ovary	ovary
23	chr2:39667000-39670600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:39667000-39670600	Weak transcription	Aorta	Aorta
25	chr2:39667000-39670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:39667000-39672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
30	chr2:39667200-39669600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:39667200-39670000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:39667200-39672400	Weak transcription	Fetal Stomach	stomach
33	chr2:39667200-39685200	Weak transcription	NHEK	skin
34	chr2:39667200-39694600	Weak transcription	NHLF	lung
35	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
36	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
37	chr2:39667400-39669400	Weak transcription	A549	lung
38	chr2:39667400-39670600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:39667400-39671000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:39667400-39671400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:39667400-39672200	Weak transcription	Brain Anterior Caudate	brain
42	chr2:39667400-39674600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:39667400-39682000	Weak transcription	HSMM	muscle
44	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:39667600-39670000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:39667600-39670800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:39667600-39672800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:39667600-39674400	Weak transcription	Osteobl	bone
50	chr2:39667600-39675000	Weak transcription	HMEC	breast

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