Variant report

Variant	rs6724393
Chromosome Location	chr2:39630391-39630392
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	chr2:39629463..39631095-chr2:39633631..39635897,2	K562	blood:
2	chr2:39621678..39625449-chr2:39627882..39630825,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10169391	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.95[AFR][1000 genomes]
rs10170604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.86[AFR][1000 genomes]
rs10175333	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.86[AFR][1000 genomes]
rs10865152	0.86[AFR][1000 genomes]
rs11124676	0.81[AFR][1000 genomes]
rs11124677	0.81[AFR][1000 genomes]
rs11124679	0.90[AFR][1000 genomes]
rs11124681	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.84[AFR][1000 genomes]
rs12712641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.86[AFR][1000 genomes]
rs2005892	0.85[AFR][1000 genomes]
rs2056654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160661	1.00[AMR][1000 genomes]
rs2178762	0.89[AFR][1000 genomes]
rs2193422	0.86[AFR][1000 genomes]
rs2373536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.89[AFR][1000 genomes]
rs4670934	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.88[AFR][1000 genomes]
rs6544223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6718134	0.81[AFR][1000 genomes]
rs6730902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.93[AFR][1000 genomes]
rs6741312	1.00[AMR][1000 genomes]
rs6742170	0.86[AFR][1000 genomes]
rs6759495	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.86[AFR][1000 genomes]
rs7578136	0.85[AFR][1000 genomes]
rs7579414	0.81[AFR][1000 genomes]
rs7582160	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7608153	0.82[AFR][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	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
3	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:39617800-39630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39618000-39633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:39620200-39635600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:39622000-39635400	Weak transcription	HSMM	muscle
9	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
10	chr2:39622800-39630400	Weak transcription	Liver	Liver
11	chr2:39622800-39630400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:39622800-39630600	Weak transcription	Fetal Stomach	stomach
13	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain
14	chr2:39622800-39643400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:39625200-39630600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:39625400-39630600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:39625400-39634400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:39626800-39630400	Weak transcription	Aorta	Aorta
19	chr2:39626800-39630600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:39626800-39634200	Weak transcription	Fetal Kidney	kidney
21	chr2:39626800-39635800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:39627000-39630400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:39627000-39630400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:39627000-39630400	Weak transcription	HMEC	breast
25	chr2:39627000-39630600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:39627000-39631400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:39627000-39632200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:39627000-39632400	Weak transcription	HSMMtube	muscle
29	chr2:39627000-39632800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:39627000-39636600	Weak transcription	Osteobl	bone
31	chr2:39627200-39633600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:39627400-39630400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:39627400-39630400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:39627400-39630400	Weak transcription	Brain Substantia Nigra	brain
35	chr2:39627400-39630400	Weak transcription	Small Intestine	intestine
36	chr2:39627400-39630600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:39627400-39630600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:39627400-39631000	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:39627400-39633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:39627400-39634800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:39627400-39635000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39627400-39636600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:39627400-39639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:39627600-39630400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:39627600-39630400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:39628000-39632800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39628200-39630800	Enhancers	Brain Anterior Caudate	brain
48	chr2:39628200-39631000	Enhancers	HUVEC	blood vessel
49	chr2:39628200-39631200	Weak transcription	Stomach Mucosa	stomach
50	chr2:39628200-39631600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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