Variant report

Variant	rs6005724
Chromosome Location	chr22:28544093-28544094
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28539281..28541367-chr22:28542040..28544765,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12157518	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12160232	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16986103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16986290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16986377	0.84[ASN][1000 genomes]
rs2345714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28462248	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs55961693	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs5997341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997355	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6005697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6005704	0.86[AFR][1000 genomes]
rs6005726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6005757	0.84[ASN][1000 genomes]
rs6005758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6005765	0.88[ASN][1000 genomes]
rs6005779	0.82[ASN][1000 genomes]
rs73427747	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7510988	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28533800-28559000	Weak transcription	Aorta	Aorta
2	chr22:28534200-28545200	Enhancers	Fetal Lung	lung
3	chr22:28536000-28544400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:28536200-28546600	Weak transcription	Left Ventricle	heart
5	chr22:28536200-28549600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr22:28537200-28558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:28538400-28544800	Weak transcription	Dnd41	blood
8	chr22:28538800-28549800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:28539200-28547000	Weak transcription	Fetal Intestine Small	intestine
10	chr22:28539200-28558400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr22:28539600-28549800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr22:28540200-28558600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr22:28540200-28567800	Weak transcription	Gastric	stomach
14	chr22:28540400-28550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:28540800-28546200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr22:28540800-28547400	Weak transcription	NHLF	lung
17	chr22:28540800-28549800	Weak transcription	Psoas Muscle	Psoas
18	chr22:28540800-28567800	Weak transcription	Small Intestine	intestine
19	chr22:28541000-28547200	Weak transcription	Right Atrium	heart
20	chr22:28541000-28553000	Weak transcription	Fetal Muscle Leg	muscle
21	chr22:28541000-28557200	Weak transcription	Lung	lung
22	chr22:28542000-28544200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:28542000-28544200	Enhancers	Brain Cingulate Gyrus	brain
24	chr22:28542200-28544200	Enhancers	Brain Angular Gyrus	brain
25	chr22:28542200-28544400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr22:28542200-28544400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:28542600-28546400	Weak transcription	HSMM	muscle
28	chr22:28542800-28548000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr22:28543000-28546800	Weak transcription	Ovary	ovary
30	chr22:28543000-28549600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr22:28543200-28548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr22:28543200-28548200	Weak transcription	Right Ventricle	heart
33	chr22:28543400-28544200	Enhancers	Brain Anterior Caudate	brain
34	chr22:28543400-28546400	Weak transcription	Colon Smooth Muscle	Colon
35	chr22:28543400-28548200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr22:28543400-28548200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr22:28543400-28550800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:28543400-28557600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:28543400-28559200	Weak transcription	Fetal Kidney	kidney
40	chr22:28543400-28568800	Weak transcription	NHDF-Ad	bronchial
41	chr22:28543600-28546600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr22:28543600-28546600	Weak transcription	Adipose Nuclei	Adipose
43	chr22:28543600-28551000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:28543600-28559000	Weak transcription	Pancreas	Pancrea
45	chr22:28543800-28545800	Weak transcription	Fetal Brain Female	brain
46	chr22:28543800-28546800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr22:28543800-28550800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr22:28543800-28551200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr22:28543800-28553600	Weak transcription	Brain Hippocampus Middle	brain
50	chr22:28543800-28558600	Weak transcription	Fetal Stomach	stomach

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