Variant report

Variant	rs7577097
Chromosome Location	chr2:39675339-39675340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39675054..39675789-chr2:39693150..39694137,5	MCF-7	breast:
2	chr2:39673697..39675458-chr2:39682024..39684470,2	MCF-7	breast:
3	chr2:39655176..39658174-chr2:39672805..39675633,2	K562	blood:
4	chr2:39673263..39677123-chr2:39692250..39696646,6	MCF-7	breast:
5	chr2:39662404..39665999-chr2:39671403..39675568,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10169501	0.90[AFR][1000 genomes]
rs10199459	1.00[EUR][1000 genomes]
rs11124683	0.94[EUR][1000 genomes]
rs11884949	1.00[ASN][1000 genomes]
rs11896389	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328714	0.94[EUR][1000 genomes]
rs17023530	0.94[EUR][1000 genomes]
rs17023542	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17023547	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17023600	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17023611	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023640	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17023684	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17023696	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17023773	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17446102	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17446515	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17446690	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17505580	0.94[EUR][1000 genomes]
rs17505877	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17531732	0.80[ASN][1000 genomes]
rs2056653	1.00[EUR][1000 genomes]
rs2056655	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2111383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373532	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs3732052	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670273	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4670938	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4670940	0.89[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs55761128	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58177306	0.80[ASN][1000 genomes]
rs59109595	0.80[ASN][1000 genomes]
rs6544227	0.97[EUR][1000 genomes]
rs6544229	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720537	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6720951	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6721740	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731310	0.85[EUR][1000 genomes]
rs6758596	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73924009	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559436	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605939	1.00[CEU][hapmap];1.00[EUR][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:62 , 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	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:39665600-39684200	Weak transcription	Lung	lung
4	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
5	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
7	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39666600-39675800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:39666800-39677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
14	chr2:39666800-39681600	Weak transcription	Ovary	ovary
15	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
18	chr2:39667200-39685200	Weak transcription	NHEK	skin
19	chr2:39667200-39694600	Weak transcription	NHLF	lung
20	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
21	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
22	chr2:39667400-39682000	Weak transcription	HSMM	muscle
23	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:39668200-39681400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:39668200-39684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:39668200-39685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
30	chr2:39668400-39676000	Weak transcription	Placenta	Placenta
31	chr2:39668400-39677000	Weak transcription	K562	blood
32	chr2:39670400-39682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:39670400-39685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:39670800-39684800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:39671000-39682200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:39671200-39681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:39671200-39685000	Weak transcription	Aorta	Aorta
38	chr2:39671600-39682600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:39671800-39682000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:39672000-39681400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39672200-39681400	Weak transcription	Adipose Nuclei	Adipose
42	chr2:39672200-39684600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:39672400-39675600	Weak transcription	Fetal Intestine Small	intestine
44	chr2:39672600-39681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:39673400-39676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:39673400-39681000	Weak transcription	Liver	Liver
47	chr2:39673600-39681000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:39674800-39675400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:39674800-39678800	Enhancers	HepG2	liver
50	chr2:39675000-39675400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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