Variant report

Variant	rs10516521
Chromosome Location	chr4:106553247-106553248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:106553120-106553270	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr4:106553240-106553510	HA-sp	spinal cord:	n/a	chr4:106553357-106553375
3	CTCF	chr4:106553140-106553290	NHEK	skin:	n/a	n/a
4	RAD21	chr4:106553165-106553452	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr4:106553220-106553370	AG09309	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106507986..106508713-chr4:106552891..106553776,2	MCF-7	breast:
2	chr4:106551066..106553304-chr4:106554764..106557065,2	K562	blood:

Variant related genes	Relation type
ARHGEF38	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10017111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10023798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10032269	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516520	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516524	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11097896	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11721732	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11721842	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11730080	0.82[ASN][1000 genomes]
rs11730082	0.82[ASN][1000 genomes]
rs11730825	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11735330	0.82[ASN][1000 genomes]
rs1294671	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1447097	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17035915	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17035936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17035939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17035951	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17259503	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17259931	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17260120	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17260183	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17260856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17261094	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17262443	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17262457	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17263714	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs17264527	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs17325276	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17326919	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327234	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862081	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1982346	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2098571	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2112047	1.00[CHB][hapmap]
rs2112049	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2161046	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2193855	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2193856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2193857	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2216515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2305212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2544401	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2544402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544403	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544417	0.82[CHB][hapmap]
rs2544418	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544424	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544426	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2544429	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553448	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553451	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2553456	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553457	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553463	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553464	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553466	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2553467	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553470	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2553471	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2866781	0.85[CEU][hapmap]
rs3796920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3796923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4324546	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4324547	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4326019	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4407508	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4588463	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs58412572	0.82[ASN][1000 genomes]
rs59936741	0.82[ASN][1000 genomes]
rs6833345	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs72669979	0.82[ASN][1000 genomes]
rs72669984	0.94[ASN][1000 genomes]
rs73837046	0.82[ASN][1000 genomes]
rs73837092	0.88[ASN][1000 genomes]
rs73837096	0.88[ASN][1000 genomes]
rs7666969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7676226	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7681991	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7687176	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7698817	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs961472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs961473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106525400-106558600	Weak transcription	Fetal Intestine Large	intestine
2	chr4:106527200-106559000	Weak transcription	Fetal Intestine Small	intestine
3	chr4:106540600-106553800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:106545200-106577800	Weak transcription	Pancreas	Pancrea
5	chr4:106545800-106558600	Weak transcription	Left Ventricle	heart
6	chr4:106546000-106553800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:106546000-106555800	Weak transcription	Fetal Lung	lung
8	chr4:106546000-106558200	Weak transcription	Brain Substantia Nigra	brain
9	chr4:106546200-106554000	Weak transcription	Small Intestine	intestine
10	chr4:106547000-106553800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:106549400-106555200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:106549600-106555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:106549600-106558600	Weak transcription	Gastric	stomach
14	chr4:106549800-106553400	Weak transcription	Stomach Mucosa	stomach
15	chr4:106550600-106559400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:106551600-106555200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:106551800-106554000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:106551800-106554800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:106551800-106555400	Enhancers	HMEC	breast
20	chr4:106552400-106555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:106552400-106555600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:106552400-106555600	Enhancers	GM12878-XiMat	blood
23	chr4:106552400-106558400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:106552600-106554200	Weak transcription	Fetal Heart	heart
25	chr4:106552600-106555000	Weak transcription	Fetal Brain Male	brain
26	chr4:106552800-106554400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:106552800-106555600	Weak transcription	Brain Anterior Caudate	brain
28	chr4:106552800-106558200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:106552800-106558400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:106552800-106558400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:106553000-106553400	Flanking Active TSS	NHEK	skin
32	chr4:106553000-106553600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr4:106553200-106554000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:106553200-106559000	Weak transcription	Fetal Kidney	kidney

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