Variant report

Variant	rs10025790
Chromosome Location	chr4:106551549-106551550
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106551066..106553304-chr4:106554764..106557065,2	K562	blood:
2	chr4:106551262..106552190-chr6:128410714..128411291,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10023798	0.80[CEU][hapmap]
rs10032142	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032283	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10034172	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516523	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs11097895	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11722731	0.82[JPT][hapmap]
rs11726715	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11934139	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs11941690	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs12639750	0.84[JPT][hapmap]
rs13138544	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13148869	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs1447093	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447094	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1447098	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447099	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447100	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447101	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17036041	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17036049	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17036098	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs17262764	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs2044536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080789	0.84[JPT][hapmap]
rs2121558	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544395	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs2553449	0.82[JPT][hapmap]
rs2553458	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs2553468	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs28415919	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796920	0.80[CEU][hapmap]
rs3822277	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484305	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699196	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs67822595	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820200	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs6833345	0.86[CEU][hapmap]
rs7684839	0.84[JPT][hapmap]
rs7685231	0.82[JPT][hapmap]
rs7686722	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699846	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921113	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9999133	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999326	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106516000-106553000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:106525400-106558600	Weak transcription	Fetal Intestine Large	intestine
3	chr4:106527200-106559000	Weak transcription	Fetal Intestine Small	intestine
4	chr4:106540600-106553800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:106542600-106551800	Weak transcription	HMEC	breast
6	chr4:106545200-106577800	Weak transcription	Pancreas	Pancrea
7	chr4:106545800-106552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:106545800-106558600	Weak transcription	Left Ventricle	heart
9	chr4:106546000-106552400	Weak transcription	Brain Anterior Caudate	brain
10	chr4:106546000-106553800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:106546000-106555800	Weak transcription	Fetal Lung	lung
12	chr4:106546000-106558200	Weak transcription	Brain Substantia Nigra	brain
13	chr4:106546200-106551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:106546200-106552000	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:106546200-106554000	Weak transcription	Small Intestine	intestine
16	chr4:106546800-106551800	Weak transcription	Fetal Heart	heart
17	chr4:106547000-106553800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:106549400-106555200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:106549600-106555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:106549600-106558600	Weak transcription	Gastric	stomach
21	chr4:106549800-106553400	Weak transcription	Stomach Mucosa	stomach
22	chr4:106550000-106551600	Weak transcription	Fetal Brain Male	brain
23	chr4:106550200-106551600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:106550600-106559400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:106551400-106552400	Weak transcription	GM12878-XiMat	blood

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