Variant report

Variant	rs1625442
Chromosome Location	chr12:44711555-44711556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:167)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:167 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:44711399-44711803	LNCaP	prostate:	n/a	n/a
2	CTCF	chr12:44711440-44711590	AG10803	skin:	n/a	n/a
3	RAD21	chr12:44711301-44711680	GM12878	blood:	n/a	n/a
4	SMC3	chr12:44711339-44711722	GM12878	blood:	n/a	n/a
5	CTCF	chr12:44711460-44711610	GM12868	blood:	n/a	n/a
6	RAD21	chr12:44711320-44711864	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr12:44711440-44711590	HRE	kidney:	n/a	n/a
8	CTCF	chr12:44711480-44711630	HCM	heart:	n/a	n/a
9	CTCF	chr12:44711365-44711557	A549	lung:	n/a	n/a
10	CTCF	chr12:44711441-44711582	Spleen_OC	spleen:	n/a	n/a
11	CTCF	chr12:44711415-44711603	GM10248	blood:	n/a	n/a
12	CTCF	chr12:44711440-44711590	HUVEC	blood vessel:	n/a	n/a
13	STAT1	chr12:44711500-44711671	GM12878	blood:	n/a	n/a
14	RAD21	chr12:44711236-44711806	HCT-116	colon:	n/a	n/a
15	CTCF	chr12:44711420-44711570	NHDF-neo	bronchial:	n/a	n/a
16	CTCF	chr12:44711386-44711801	MCF-7	breast:	n/a	n/a
17	CTCF	chr12:44711460-44711610	HEEpiC	esophagus:	n/a	n/a
18	CTCF	chr12:44711420-44711570	GM12867	blood:	n/a	n/a
19	CTCF	chr12:44711460-44711610	GM12872	blood:	n/a	n/a
20	CTCF	chr12:44711386-44711649	GM12878	blood:	n/a	n/a
21	RAD21	chr12:44711351-44711902	ECC-1	luminal epithelium:	n/a	n/a
22	FOXA1	chr12:44711442-44711694	T-47D	breast:	n/a	n/a
23	CTCF	chr12:44711408-44711654	Kidney_OC	kidney:	n/a	n/a
24	RAD21	chr12:44711389-44711783	MCF-7	breast:	n/a	n/a
25	CTCF	chr12:44711388-44711618	MCF-7	breast:	n/a	n/a
26	CTCF	chr12:44711420-44711570	HA-sp	spinal cord:	n/a	n/a
27	CTCF	chr12:44711440-44711590	HMEC	breast:	n/a	n/a
28	CTCF	chr12:44711440-44711590	AoAF	blood vessel:	n/a	n/a
29	CTCF	chr12:44711401-44711627	GM13977	blood:	n/a	n/a
30	RAD21	chr12:44711364-44711829	MCF-7	breast:	n/a	n/a
31	CTCF	chr12:44711363-44711645	HepG2	liver:	n/a	n/a
32	CTCF	chr12:44711420-44711570	GM12871	blood:	n/a	n/a
33	CTCF	chr12:44711420-44711570	HAc	cerebellar:	n/a	n/a
34	CTCF	chr12:44711460-44711610	NHEK	skin:	n/a	n/a
35	CTCF	chr12:44711480-44711630	BJ	skin:	n/a	n/a
36	CTCF	chr12:44711460-44711610	AG10803	skin:	n/a	n/a
37	CTCF	chr12:44711416-44711760	A549	lung:	n/a	n/a
38	CTCF	chr12:44711480-44711630	HCPEpiC	choroid plexus:	n/a	n/a
39	CTCF	chr12:44711411-44711849	MCF-7	breast:	n/a	n/a
40	CTCF	chr12:44711440-44711590	HEK293	kidney:	n/a	n/a
41	CTCF	chr12:44711420-44711570	Caco-2	colon:	n/a	n/a
42	RAD21	chr12:44711311-44711822	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr12:44711420-44711570	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr12:44711440-44711590	HPAF	blood vessel:	n/a	n/a
45	CTCF	chr12:44711500-44711650	GM12868	blood:	n/a	n/a
46	CTCF	chr12:44711480-44711630	GM12872	blood:	n/a	n/a
47	CTCF	chr12:44711420-44711570	HFF-Myc	foreskin:	n/a	n/a
48	CTCF	chr12:44711420-44711570	GM12865	blood:	n/a	n/a
49	CTCF	chr12:44711460-44711610	GM12870	blood:	n/a	n/a
50	RAD21	chr12:44711152-44711964	SK-N-SH	brain:	n/a	n/a

No data

Variant related genes	Relation type
TMEM117	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10506245	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1098497	1.00[ASN][1000 genomes]
rs1527315	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1622682	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1643432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1643433	1.00[ASN][1000 genomes]
rs1643434	1.00[ASN][1000 genomes]
rs1644007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1644009	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1644010	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1644011	0.83[ASN][1000 genomes]
rs1644014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1716606	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716609	1.00[CHB][hapmap]
rs1726874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1726879	1.00[ASN][1000 genomes]
rs1726884	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1726887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1726888	1.00[ASN][1000 genomes]
rs1726889	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1726890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1726900	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798020	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1798023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798025	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798026	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798027	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798032	1.00[CHB][hapmap]
rs58802461	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60441308	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314412	1.00[CHB][hapmap]
rs73274199	0.83[ASN][1000 genomes]
rs73276236	1.00[ASN][1000 genomes]
rs73276240	1.00[ASN][1000 genomes]
rs73276275	1.00[ASN][1000 genomes]
rs7958975	1.00[ASN][1000 genomes]
rs7974460	1.00[CHD][hapmap]
rs840764	1.00[ASN][1000 genomes]
rs840766	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840767	1.00[ASN][1000 genomes]
rs840768	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840772	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs840773	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs840774	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs859016	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs863482	1.00[CHB][hapmap];1.00[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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1038498	chr12:44679455-44816572	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv520635	chr12:44707667-44720874	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44699000-44712600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:44699000-44713800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:44699000-44736000	Weak transcription	Pancreas	Pancrea
4	chr12:44699000-44782000	Weak transcription	Aorta	Aorta
5	chr12:44703400-44711800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:44706800-44711800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:44709200-44743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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