Variant report

Variant	rs9968420
Chromosome Location	chr4:126364565-126364566
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	chr4:126363138..126365093-chr4:126372306..126373969,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10014217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10084892	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939811	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11944077	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12498276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12501179	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12504612	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511204	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512105	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009520	0.90[CHD][hapmap]
rs17009618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009635	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009673	0.91[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2710562	0.85[CHB][hapmap]
rs4272024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4833325	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58972262	0.82[ASN][1000 genomes]
rs59208392	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840704	0.81[ASN][1000 genomes]
rs73849218	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73849222	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73849223	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126334600-126390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr4:126335200-126400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:126338600-126371000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:126338800-126371400	Weak transcription	Fetal Intestine Large	intestine
5	chr4:126342400-126375400	Weak transcription	Right Ventricle	heart
6	chr4:126342600-126371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:126345000-126369600	Weak transcription	Ovary	ovary
8	chr4:126345000-126371400	Weak transcription	Fetal Stomach	stomach
9	chr4:126345000-126371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:126345000-126373200	Weak transcription	Lung	lung
11	chr4:126345600-126369400	Weak transcription	Fetal Kidney	kidney
12	chr4:126345600-126369600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:126345600-126369600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:126347800-126382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:126351600-126369400	Weak transcription	Fetal Brain Female	brain
16	chr4:126353400-126373000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:126353600-126367400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:126353600-126371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:126353600-126377000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:126355000-126369600	Weak transcription	NHLF	lung
21	chr4:126355000-126399600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:126355200-126369400	Weak transcription	HUVEC	blood vessel
23	chr4:126355600-126369800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:126356000-126369800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:126356000-126391600	Weak transcription	HSMM	muscle
26	chr4:126356200-126370600	Weak transcription	Aorta	Aorta
27	chr4:126356200-126370600	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:126356400-126369800	Weak transcription	Adipose Nuclei	Adipose
29	chr4:126356400-126414200	Weak transcription	Osteobl	bone
30	chr4:126357000-126367400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:126357000-126369600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:126357000-126370000	Weak transcription	Liver	Liver
33	chr4:126358200-126369600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:126358800-126369600	Weak transcription	Left Ventricle	heart
35	chr4:126359000-126367200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:126361800-126373200	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:126362400-126368600	Weak transcription	Fetal Brain Male	brain
38	chr4:126362800-126365800	Strong transcription	Fetal Lung	lung
39	chr4:126363000-126366400	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:126363200-126365400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:126364400-126364800	Enhancers	Duodenum Smooth Muscle	Duodenum

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