Variant report

Variant	rs10169391
Chromosome Location	chr2:39675796-39675797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39673263..39677123-chr2:39692250..39696646,6	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10170424	0.87[AFR][1000 genomes]
rs10170604	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.81[AFR][1000 genomes]
rs10175333	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.81[AFR][1000 genomes]
rs10865152	0.81[AFR][1000 genomes]
rs11124679	0.85[AFR][1000 genomes]
rs11124681	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.82[AFR][1000 genomes]
rs12712641	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474424	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.81[AFR][1000 genomes]
rs2056654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	1.00[AMR][1000 genomes]
rs2160661	1.00[AMR][1000 genomes]
rs2178762	0.84[AFR][1000 genomes]
rs2193422	0.81[AFR][1000 genomes]
rs2373536	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.84[AFR][1000 genomes]
rs4670934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.83[AFR][1000 genomes]
rs6544223	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6724393	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.85[AFR][1000 genomes]
rs6741312	1.00[AMR][1000 genomes]
rs6742170	0.81[AFR][1000 genomes]
rs6759495	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.81[AFR][1000 genomes]
rs7582160	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:60 , 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	chr2:39672600-39681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:39673400-39676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:39673400-39681000	Weak transcription	Liver	Liver
46	chr2:39673600-39681000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39674800-39678800	Enhancers	HepG2	liver
48	chr2:39675000-39675800	Flanking Active TSS	A549	lung
49	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
50	chr2:39675200-39677800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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