Variant report

Variant	rs786447
Chromosome Location	chr12:124069667-124069668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:102)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:102 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:124069137-124069728	GM12878	blood:	n/a	chr12:124069466-124069475
2	POLR2A	chr12:124068654-124069793	HL-60	blood:	n/a	n/a
3	REST	chr12:124069168-124069769	HL-60	blood:	n/a	chr12:124069466-124069475
4	POLR2A	chr12:124068566-124069688	GM18951	blood:	n/a	n/a
5	POLR2A	chr12:124068438-124069783	K562	blood:	n/a	n/a
6	POLR2A	chr12:124068520-124070709	SK-N-MC	brain:	n/a	n/a
7	MAX	chr12:124068737-124069838	K562	blood:	n/a	n/a
8	POLR2A	chr12:124069627-124073859	K562	blood:	n/a	n/a
9	SIN3AK20	chr12:124069433-124069750	SK-N-SH	brain:	n/a	n/a
10	MXI1	chr12:124069555-124069861	K562	blood:	n/a	n/a
11	REST	chr12:124069158-124069831	H1-hESC	embryonic stem cell:	n/a	chr12:124069466-124069475
12	MAX	chr12:124068671-124069771	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr12:124069662-124069909	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr12:124068684-124069950	HL-60	blood:	n/a	chr12:124069466-124069475
15	HA-E2F1	chr12:124069512-124069950	MCF-7	breast:	n/a	chr12:124069540-124069555 chr12:124069545-124069552 chr12:124069545-124069552 chr12:124069544-124069556 chr12:124069693-124069700 chr12:124069545-124069552
16	SIN3AK20	chr12:124068706-124069874	K562	blood:	n/a	n/a
17	MYC	chr12:124068589-124069894	K562	blood:	n/a	n/a
18	REST	chr12:124068675-124069688	PANC-1	pancreas:	n/a	chr12:124069466-124069475
19	MAX	chr12:124068456-124069877	A549	lung:	n/a	n/a
20	ETS1	chr12:124068724-124069699	K562	blood:	n/a	n/a
21	SIN3AK20	chr12:124069542-124069734	HepG2	liver:	n/a	n/a
22	MAX	chr12:124068578-124069800	ECC-1	luminal epithelium:	n/a	n/a
23	REST	chr12:124069236-124069819	MCF-7	breast:	n/a	chr12:124069466-124069475
24	MYC	chr12:124068621-124069972	K562	blood:	n/a	n/a
25	MXI1	chr12:124068691-124069985	HepG2	liver:	n/a	n/a
26	SIN3A	chr12:124068728-124070099	H1-hESC	embryonic stem cell:	n/a	n/a
27	MTA3	chr12:124068553-124069799	GM12878	blood:	n/a	n/a
28	REST	chr12:124068622-124069783	PFSK-1	brain:	n/a	chr12:124069466-124069475
29	MXI1	chr12:124068803-124069779	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr12:124068442-124070037	A549	lung:	n/a	n/a
31	POLR2A	chr12:124068610-124069883	HL-60	blood:	n/a	n/a
32	MXI1	chr12:124068488-124070795	IMR90	lung:	n/a	n/a
33	REST	chr12:124068656-124069859	K562	blood:	n/a	chr12:124069466-124069475
34	POLR2A	chr12:124068417-124069705	HUVEC	blood vessel:	n/a	n/a
35	UBTF	chr12:124068570-124070035	K562	blood:	n/a	n/a
36	MAX	chr12:124068731-124070113	K562	blood:	n/a	n/a
37	MAZ	chr12:124068779-124069759	K562	blood:	n/a	n/a
38	POLR2A	chr12:124069625-124070734	PFSK-1	brain:	n/a	n/a
39	HCFC1	chr12:124068422-124070407	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:124068496-124070077	K562	blood:	n/a	n/a
41	MYC	chr12:124068770-124069927	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr12:124068404-124070969	HepG2	liver:	n/a	n/a
43	REST	chr12:124068981-124069669	PANC-1	pancreas:	n/a	chr12:124069466-124069475
44	MXI1	chr12:124068656-124070224	GM12878	blood:	n/a	n/a
45	MAX	chr12:124068855-124069748	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr12:124068719-124069742	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr12:124069519-124069989	GM12878	blood:	n/a	n/a
48	REST	chr12:124068677-124069798	ECC-1	luminal epithelium:	n/a	chr12:124069466-124069475
49	E2F6	chr12:124069570-124069815	K562	blood:	n/a	chr12:124069693-124069700
50	POLR2A	chr12:124068634-124069675	NB4	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:124069649-124069699	NHDF-neo	bronchial:	n/a
2	chr12:124069649-124069699	HCF	heart:	n/a
3	chr12:124069649-124069699	HEEpiC	esophagus:	n/a
4	chr12:124069649-124069699	HepG2	liver:	n/a
5	chr12:124069649-124069699	GM12891	blood:	n/a
6	chr12:124069649-124069699	PrEC	prostate:	n/a
7	chr12:124069649-124069699	AG04450	lung:	fetal
8	chr12:124069649-124069699	SKMC	muscle:	n/a
9	chr12:124069649-124069699	HRCEpiC	kidney:	n/a
10	chr12:124069649-124069699	Hela-S3	cervix:	n/a
11	chr12:124069649-124069699	HNPCEpiC	eye:	n/a
12	chr12:124069649-124069699	PFSK-1	brain:	n/a
13	chr12:124069649-124069699	AG10803	skin:	n/a
14	chr12:124069649-124069699	AoSMC	blood vessel:	n/a
15	chr12:124069649-124069699	GM12878	blood:	n/a
16	chr12:124069649-124069699	BE2_C	brain:	n/a
17	chr12:124069649-124069699	H1-hESC	embryonic stem cell:	embryo
18	chr12:124069649-124069699	HRPEpiC	eye:	n/a
19	chr12:124069649-124069699	ECC-1	luminal epithelium:	n/a
20	chr12:124069649-124069699	AG09309	skin:	n/a
21	chr12:124069649-124069699	ProgFib	skin:	n/a
22	chr12:124069649-124069699	HCPEpiC	choroid plexus:	n/a
23	chr12:124069649-124069699	SK-N-SH	brain:	n/a
24	chr12:124069649-124069699	ovcar-3	ovarian:	n/a
25	chr12:124069649-124069699	CMK	blood:	n/a
26	chr12:124069649-124069699	MCF10A-Er-Src	breast:	n/a
27	chr12:124069649-124069699	HEK293	kidney:	embryo
28	chr12:124069649-124069699	Jurkat	blood:	n/a
29	chr12:124069649-124069699	HCM	heart:	n/a
30	chr12:124069649-124069699	MCF-7	breast:	n/a
31	chr12:124069649-124069699	U87	brain:	n/a
32	chr12:124069649-124069699	AG04449	skin:	fetal
33	chr12:124069649-124069699	NB4	blood:	n/a
34	chr12:124069649-124069699	PANC-1	pancreas:	n/a
35	chr12:124069649-124069699	HMEC	breast:	n/a
36	chr12:124069649-124069699	HRE	kidney:	n/a
37	chr12:124069649-124069699	T-47D	breast:	n/a
38	chr12:124069649-124069699	HUVEC	blood vessel:	n/a
39	chr12:124069649-124069699	K562	blood:	n/a
40	chr12:124069649-124069699	LNCaP	prostate:	n/a
41	chr12:124069649-124069699	NH-A	brain:	n/a
42	chr12:124069649-124069699	GM06990	blood:	n/a
43	chr12:124069649-124069699	AG09319	gingival:	n/a
44	chr12:124069649-124069699	GM12892	blood:	n/a
45	chr12:124069649-124069699	HL-60	blood:	n/a
46	chr12:124069649-124069699	Hepatocyte	liver:	n/a
47	chr12:124069649-124069699	IMR90	lung:	fetal
48	chr12:124069649-124069699	HIPEpiC	eye:	n/a
49	chr12:124069649-124069699	SK-N-SH_RA	brain:	n/a
50	chr12:124069649-124069699	NT2-D1	testis:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
2	chr12:123920837..123922890-chr12:124067881..124069805,2	K562	blood:
3	chr12:123755285..123757528-chr12:124068793..124071301,3	MCF-7	breast:
4	chr12:123941098..123944051-chr12:124068238..124070527,2	K562	blood:
5	chr12:124067567..124070616-chr12:124116717..124118360,3	K562	blood:
6	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
7	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
8	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
9	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
10	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
11	chr12:124067553..124070106-chr12:124116767..124119854,4	MCF-7	breast:
12	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
13	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
14	chr12:123753500..123755086-chr12:124068992..124070507,2	MCF-7	breast:
15	chr12:124018224..124020563-chr12:124065688..124070487,5	K562	blood:
16	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

No data

Variant related genes	Relation type
TMED2	TF binding region
ENSG00000247373	TF binding region
ENSG00000247373	CpG island
TMED2	CpG island
ENSG00000111361	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000150977	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1057879	1.00[JPT][hapmap]
rs10846531	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs10846535	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057297	1.00[JPT][hapmap]
rs11057307	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11615300	0.81[EUR][1000 genomes]
rs1515814	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048802	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2333831	1.00[JPT][hapmap]
rs3748268	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs3748269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850952	1.00[JPT][hapmap]
rs4040225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930713	1.00[JPT][hapmap]
rs4930714	1.00[JPT][hapmap]
rs6488883	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7966882	0.83[EUR][1000 genomes]
rs7972413	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs908373	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9919	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs786447	TCTN2	cis	Artery Tibial	GTEx
rs786447	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124066400-124070000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:124066800-124069800	Active TSS	HSMM	muscle
3	chr12:124066800-124070000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:124066800-124070000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:124066800-124070000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:124067000-124069800	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:124067000-124070000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:124067000-124070000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:124067000-124070400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:124067200-124069800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:124067200-124070000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:124067200-124070400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:124067200-124070600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:124067400-124069800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:124067400-124069800	Active TSS	NHEK	skin
16	chr12:124067400-124070000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:124067400-124070000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:124067400-124070000	Active TSS	HMEC	breast
19	chr12:124067400-124070000	Active TSS	NHDF-Ad	bronchial
20	chr12:124067400-124070200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:124067400-124070200	Active TSS	A549	lung
22	chr12:124067400-124070800	Active TSS	NHLF	lung
23	chr12:124067600-124069800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:124067600-124069800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:124067600-124069800	Active TSS	Small Intestine	intestine
26	chr12:124067600-124070000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:124067600-124070000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:124067600-124070000	Active TSS	Hela-S3	cervix
29	chr12:124067600-124070000	Active TSS	Osteobl	bone
30	chr12:124067600-124070200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr12:124067600-124070200	Active TSS	Aorta	Aorta
32	chr12:124067600-124070200	Active TSS	Fetal Intestine Large	intestine
33	chr12:124067600-124070400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:124067600-124070400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:124067600-124071400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:124067800-124069800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:124067800-124069800	Active TSS	GM12878-XiMat	blood
38	chr12:124067800-124070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:124067800-124070000	Active TSS	Muscle Satellite Cultured Cells	--
40	chr12:124067800-124070000	Active TSS	HSMMtube	muscle
41	chr12:124067800-124070000	Active TSS	K562	blood
42	chr12:124068000-124069800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:124068000-124069800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:124068000-124069800	Active TSS	Brain Angular Gyrus	brain
45	chr12:124068000-124069800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:124068000-124069800	Active TSS	Colonic Mucosa	Colon
47	chr12:124068000-124069800	Active TSS	Colon Smooth Muscle	Colon
48	chr12:124068000-124069800	Active TSS	Fetal Brain Female	brain
49	chr12:124068000-124069800	Active TSS	Placenta	Placenta
50	chr12:124068000-124069800	Active TSS	Fetal Stomach	stomach

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