Variant report

Variant	rs17408624
Chromosome Location	chr4:78665393-78665394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78665271..78668242-chr4:78674089..78675600,2	MCF-7	breast:
2	chr4:78664695..78666373-chr4:78741463..78744231,2	K562	blood:
3	chr4:78660857..78662460-chr4:78663917..78665509,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1058746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932644	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11941918	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11944704	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1354100	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17002830	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17409255	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17409708	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17409820	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17448620	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17448771	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17449827	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1801350	0.86[AMR][1000 genomes]
rs1915587	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1915588	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36124924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41437548	1.00[CEU][hapmap]
rs6812768	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6816113	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7656101	1.00[CEU][hapmap]
rs7657481	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7657902	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7674271	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7687500	1.00[CEU][hapmap]

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	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
3	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
6	chr4:78643800-78714000	Weak transcription	Lung	lung
7	chr4:78644800-78666600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
9	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
12	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
13	chr4:78650200-78673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:78650200-78673000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:78650200-78697800	Weak transcription	Gastric	stomach
16	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
19	chr4:78650600-78665800	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:78653200-78673200	Weak transcription	Fetal Heart	heart
22	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
23	chr4:78656600-78667800	Strong transcription	Fetal Thymus	thymus
24	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
25	chr4:78657400-78673000	Weak transcription	Fetal Intestine Small	intestine
26	chr4:78658600-78669400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:78659000-78676600	Weak transcription	Fetal Stomach	stomach
28	chr4:78659200-78673000	Strong transcription	Primary B cells from cord blood	blood
29	chr4:78659600-78671400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:78659600-78672000	Weak transcription	GM12878-XiMat	blood
31	chr4:78659600-78673000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:78659800-78676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
34	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
35	chr4:78660200-78667800	Weak transcription	NHLF	lung
36	chr4:78662000-78666600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:78662000-78695600	Weak transcription	Ovary	ovary
38	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
39	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
40	chr4:78662200-78668600	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:78662200-78682400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:78662400-78673000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:78662600-78672400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:78662600-78679800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:78662800-78665800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:78662800-78667000	Weak transcription	HepG2	liver
48	chr4:78662800-78671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:78662800-78672000	Weak transcription	Fetal Lung	lung
50	chr4:78662800-78673000	Weak transcription	Aorta	Aorta

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