Variant report

Variant	rs10023798
Chromosome Location	chr4:106547791-106547792
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106546192..106549061-chr4:106551188..106555603,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236699	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10017111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10025790	0.80[CEU][hapmap]
rs10032269	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10516519	0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs10516520	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10516521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10516524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11097896	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11721732	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11721842	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11730080	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11730082	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11730825	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11735330	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1294671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1374530	0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs1447093	0.85[CEU][hapmap]
rs1447094	0.87[CEU][hapmap]
rs1447097	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035915	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035939	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035951	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17036098	0.81[CEU][hapmap]
rs17259503	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17259931	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17260120	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17260183	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17260856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17261094	0.94[ASN][1000 genomes]
rs17261786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17262443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17262457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17263714	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17264527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17325276	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17326919	0.94[ASN][1000 genomes]
rs17327234	0.94[ASN][1000 genomes]
rs1862081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1982346	0.82[ASN][1000 genomes]
rs2044536	0.86[CEU][hapmap]
rs2098571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2112047	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs2112049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2161046	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2193856	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2193857	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2305212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544401	1.00[JPT][hapmap]
rs2544402	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544417	0.85[CEU][hapmap]
rs2544418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553446	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553448	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553451	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553460	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553461	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553463	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553464	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553471	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28536076	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4324546	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4324547	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4326019	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4407508	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4588463	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs58412572	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59428412	0.85[AMR][1000 genomes]
rs59936741	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6833345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72669979	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72669984	1.00[ASN][1000 genomes]
rs73837046	0.88[ASN][1000 genomes]
rs73837092	0.82[ASN][1000 genomes]
rs73837096	0.82[ASN][1000 genomes]
rs7666969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7676226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7681991	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7687176	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7698817	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs961472	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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:23 , 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	chr4:106545800-106548800	Weak transcription	Gastric	stomach
8	chr4:106545800-106552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:106545800-106558600	Weak transcription	Left Ventricle	heart
10	chr4:106546000-106552400	Weak transcription	Brain Anterior Caudate	brain
11	chr4:106546000-106553800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:106546000-106555800	Weak transcription	Fetal Lung	lung
13	chr4:106546000-106558200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:106546200-106549400	Weak transcription	Stomach Mucosa	stomach
15	chr4:106546200-106551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:106546200-106552000	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:106546200-106554000	Weak transcription	Small Intestine	intestine
18	chr4:106546600-106548800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:106546800-106548600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:106546800-106550600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:106546800-106551800	Weak transcription	Fetal Heart	heart
22	chr4:106547000-106548200	Weak transcription	GM12878-XiMat	blood
23	chr4:106547000-106553800	Weak transcription	Duodenum Mucosa	Duodenum

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