Variant report

Variant	rs12407684
Chromosome Location	chr1:180511823-180511824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr1:180511823-180512160	K562	blood:	n/a	n/a
2	TAF7	chr1:180511783-180512165	K562	blood:	n/a	n/a
3	GTF2B	chr1:180511737-180512067	K562	blood:	n/a	n/a
4	CTCF	chr1:180511780-180511930	AoAF	blood vessel:	n/a	n/a
5	POLR2A	chr1:180511793-180512304	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr1:180511820-180511970	AG10803	skin:	n/a	n/a
7	HEY1	chr1:180511744-180512270	K562	blood:	n/a	n/a
8	CTCF	chr1:180511760-180511910	AG04450	lung:	n/a	n/a
9	POLR2A	chr1:180511754-180512283	K562	blood:	n/a	n/a
10	CTCF	chr1:180511780-180511930	BJ	skin:	n/a	n/a
11	TEAD4	chr1:180511207-180511899	ECC-1	luminal epithelium:	n/a	chr1:180511504-180511513
12	TBP	chr1:180511685-180512066	K562	blood:	n/a	n/a
13	POLR2A	chr1:180511785-180512101	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF7	chr1:180511732-180512123	H1-hESC	embryonic stem cell:	n/a	n/a
15	EP300	chr1:180511194-180511902	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr1:180511800-180511950	AG09319	gingival:	n/a	n/a
17	POLR2A	chr1:180511708-180512258	K562	blood:	n/a	n/a
18	CTCF	chr1:180511800-180511950	AG10803	skin:	n/a	n/a
19	POLR2A	chr1:180511822-180512083	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180511395..180514188-chr1:180783985..180786756,2	K562	blood:
2	chr1:180511669..180514906-chr1:180530245..180533112,3	K562	blood:
3	chr1:180507839..180510458-chr1:180510629..180513153,2	K562	blood:
4	chr1:180511015..180513302-chr1:180517883..180519397,2	K562	blood:
5	chr1:180509296..180511935-chr1:180795313..180796906,2	K562	blood:
6	chr1:180505841..180513650-chr1:180514886..180521271,14	K562	blood:
7	chr1:180505455..180510458-chr1:180510629..180513153,4	K562	blood:
8	chr1:180501651..180503663-chr1:180510175..180512721,2	K562	blood:
9	chr1:180510781..180513155-chr1:180847874..180850004,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266683	TF binding region
ENSG00000266683	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10913975	0.82[CHB][hapmap]
rs10913977	0.87[JPT][hapmap]
rs10914021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10914022	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10914035	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10914036	0.81[CEU][hapmap]
rs10914038	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027878	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039331	0.85[CEU][hapmap]
rs12044653	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045365	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13374104	0.84[TSI][hapmap]
rs13374665	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs13376342	0.80[EUR][1000 genomes]
rs1416822	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16856127	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17300340	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17300579	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17300600	1.00[CEU][hapmap]
rs17300712	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17372295	1.00[CEU][hapmap]
rs17372362	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17372667	0.80[EUR][1000 genomes]
rs4405110	1.00[CEU][hapmap]
rs4446932	0.86[EUR][1000 genomes]
rs4651065	0.80[EUR][1000 genomes]
rs4652509	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57537558	0.86[EUR][1000 genomes]
rs58047798	0.86[EUR][1000 genomes]
rs58089956	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59022209	0.80[EUR][1000 genomes]
rs60927564	0.85[EUR][1000 genomes]
rs61388681	0.81[EUR][1000 genomes]
rs6425643	0.84[EUR][1000 genomes]
rs6425646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6684596	0.88[CHB][hapmap]
rs6694454	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697232	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72716625	0.80[EUR][1000 genomes]
rs72716629	0.80[EUR][1000 genomes]
rs72716632	0.80[EUR][1000 genomes]
rs72720914	0.86[EUR][1000 genomes]
rs7512134	0.85[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7513944	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs7517775	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs7525689	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7541993	0.81[CEU][hapmap]
rs7546119	0.81[CEU][hapmap]
rs7547266	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7551178	0.81[CEU][hapmap]
rs7552084	0.89[GIH][hapmap]
rs946631	0.81[CEU][hapmap]
rs946636	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs961162	0.85[EUR][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12407684	FAM163A	cis	cerebellum	SCAN
rs12407684	ACBD6	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180506200-180513200	Weak transcription	Pancreas	Pancrea
2	chr1:180507000-180514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180508000-180513200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:180508800-180513000	Enhancers	Fetal Heart	heart
5	chr1:180509400-180512800	Enhancers	Osteobl	bone
6	chr1:180509400-180513400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:180509600-180512200	Enhancers	HSMMtube	muscle
8	chr1:180510000-180512200	Enhancers	K562	blood
9	chr1:180510200-180512200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr1:180510200-180512600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:180510200-180516000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:180510400-180513000	Enhancers	Fetal Brain Male	brain
13	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180510800-180512000	Weak transcription	Brain Germinal Matrix	brain
15	chr1:180511000-180512000	Enhancers	Left Ventricle	heart
16	chr1:180511000-180512200	Enhancers	Adipose Nuclei	Adipose
17	chr1:180511000-180512400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:180511000-180513400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:180511200-180512000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:180511200-180512000	Enhancers	Fetal Stomach	stomach
21	chr1:180511200-180512200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:180511200-180512200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:180511200-180512200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:180511200-180512200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:180511200-180512200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:180511200-180512200	Enhancers	Aorta	Aorta
27	chr1:180511200-180512200	Enhancers	Fetal Brain Female	brain
28	chr1:180511200-180512200	Enhancers	Ovary	ovary
29	chr1:180511200-180512200	Enhancers	Right Ventricle	heart
30	chr1:180511200-180512200	Enhancers	NH-A	brain
31	chr1:180511200-180512400	Enhancers	Fetal Muscle Leg	muscle
32	chr1:180511200-180512400	Enhancers	HSMM	muscle
33	chr1:180511200-180512600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:180511200-180512800	Enhancers	Colon Smooth Muscle	Colon
35	chr1:180511200-180512800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:180511200-180513400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:180511200-180513400	Enhancers	Brain Anterior Caudate	brain
38	chr1:180511400-180512000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:180511400-180512000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:180511400-180512000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:180511400-180512000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:180511400-180512200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:180511400-180512200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:180511400-180512200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:180511400-180512200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:180511400-180512200	Enhancers	Brain Angular Gyrus	brain
47	chr1:180511400-180512800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:180511600-180512200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr1:180511600-180512200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:180511600-180513200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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