Variant report

Variant	rs10255606
Chromosome Location	chr7:12624843-12624844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:12624718-12624910	K562	blood:	n/a	n/a
2	JUND	chr7:12624596-12624889	K562	blood:	n/a	chr7:12624598-12624606
3	POLR2A	chr7:12624583-12624897	K562	blood:	n/a	n/a
4	SPI1	chr7:12624558-12624889	GM12878	blood:	n/a	n/a
5	USF2	chr7:12624698-12624982	Hela-S3	cervix:	n/a	n/a
6	IRF1	chr7:12624602-12624914	K562	blood:	n/a	n/a
7	SRF	chr7:12624671-12624874	GM12878	blood:	n/a	n/a
8	MAX	chr7:12624528-12625024	K562	blood:	n/a	n/a
9	PAX5	chr7:12624478-12624970	GM12878	blood:	n/a	n/a
10	SPI1	chr7:12624332-12625238	GM12878	blood:	n/a	n/a
11	RCOR1	chr7:12624602-12624920	K562	blood:	n/a	n/a
12	CEBPB	chr7:12624748-12625007	A549	lung:	n/a	n/a
13	EP300	chr7:12624593-12624938	GM12878	blood:	n/a	n/a
14	EP300	chr7:12624612-12624995	GM12878	blood:	n/a	n/a
15	MYC	chr7:12624521-12624973	K562	blood:	n/a	n/a
16	MAX	chr7:12624637-12624936	GM12878	blood:	n/a	n/a
17	SPI1	chr7:12624446-12624959	GM12891	blood:	n/a	n/a
18	REST	chr7:12624585-12624930	Hela-S3	cervix:	n/a	n/a
19	SPI1	chr7:12624585-12624936	K562	blood:	n/a	n/a
20	CEBPB	chr7:12624743-12624997	Hela-S3	cervix:	n/a	n/a
21	MAX	chr7:12624590-12624947	NB4	blood:	n/a	n/a
22	MAX	chr7:12624780-12624878	A549	lung:	n/a	n/a
23	BHLHE40	chr7:12624624-12625060	GM12878	blood:	n/a	n/a
24	NFYB	chr7:12624588-12624876	GM12878	blood:	n/a	n/a
25	CEBPB	chr7:12624725-12624936	HepG2	liver:	n/a	n/a
26	TBP	chr7:12624573-12624884	K562	blood:	n/a	n/a
27	ELK1	chr7:12624783-12624952	K562	blood:	n/a	n/a
28	MYC	chr7:12624559-12624932	K562	blood:	n/a	n/a
29	RUNX3	chr7:12624535-12624980	GM12878	blood:	n/a	n/a
30	SRF	chr7:12624736-12624894	GM12878	blood:	n/a	n/a
31	CUX1	chr7:12624710-12624938	K562	blood:	n/a	n/a
32	BHLHE40	chr7:12624547-12625046	K562	blood:	n/a	n/a
33	MAFF	chr7:12624538-12624866	K562	blood:	n/a	n/a
34	MAZ	chr7:12624684-12625010	K562	blood:	n/a	n/a
35	ZNF384	chr7:12624591-12624900	GM12878	blood:	n/a	n/a
36	SPI1	chr7:12624548-12624895	GM12878	blood:	n/a	n/a
37	RCOR1	chr7:12624637-12624900	GM12878	blood:	n/a	n/a
38	MAFK	chr7:12624729-12624869	Hela-S3	cervix:	n/a	n/a
39	BATF	chr7:12624569-12624895	GM12878	blood:	n/a	n/a
40	SRF	chr7:12624644-12624904	GM12878	blood:	n/a	n/a
41	EP300	chr7:12624628-12625126	K562	blood:	n/a	n/a
42	SPI1	chr7:12624481-12625091	HL-60	blood:	n/a	n/a
43	EP300	chr7:12624651-12624920	GM12878	blood:	n/a	n/a
44	CUX1	chr7:12624597-12624876	GM12878	blood:	n/a	n/a
45	NFIC	chr7:12624530-12624927	GM12878	blood:	n/a	n/a
46	ELF1	chr7:12624584-12625019	K562	blood:	n/a	n/a
47	SPI1	chr7:12624469-12625027	HL-60	blood:	n/a	n/a
48	MAX	chr7:12624617-12624973	K562	blood:	n/a	n/a
49	SPI1	chr7:12624564-12624925	K562	blood:	n/a	n/a
50	HCFC1	chr7:12624657-12624895	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12623803..12625558-chr7:12629908..12631864,2	K562	blood:
2	chr7:12623803..12627040-chr7:12629908..12631864,3	K562	blood:

No data

Variant related genes	Relation type
SCIN	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10233337	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10248988	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10276226	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1129315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17283696	0.91[JPT][hapmap]
rs1859989	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859990	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990223	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1990224	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1990225	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2215063	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240571	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240574	0.96[CEU][hapmap]
rs2240575	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3173628	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735221	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3807863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41379149	0.92[CEU][hapmap]
rs4361677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460965	0.93[CEU][hapmap]
rs6460967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6460968	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6954111	0.92[CEU][hapmap]
rs6954578	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6972477	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73293093	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7801351	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7811582	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs968792	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10255606	SCIN	cis	Thyroid	GTEx
rs10255606	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
2	chr7:12619800-12630400	Weak transcription	Esophagus	oesophagus
3	chr7:12620600-12626600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:12620800-12625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:12621800-12625600	Enhancers	Hela-S3	cervix
6	chr7:12622000-12625600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:12622600-12625000	Enhancers	Duodenum Mucosa	Duodenum
8	chr7:12623000-12625200	Enhancers	Stomach Mucosa	stomach
9	chr7:12623400-12628000	Weak transcription	Placenta	Placenta
10	chr7:12623800-12625200	Enhancers	Small Intestine	intestine
11	chr7:12624200-12625200	Enhancers	HSMMtube	muscle
12	chr7:12624200-12625400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr7:12624200-12625600	Enhancers	Adipose Nuclei	Adipose
14	chr7:12624400-12625000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:12624400-12625000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:12624400-12625000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:12624400-12625000	Enhancers	GM12878-XiMat	blood
18	chr7:12624400-12625000	Flanking Active TSS	K562	blood
19	chr7:12624400-12625000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr7:12624400-12625200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:12624400-12626000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr7:12624600-12625000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:12624600-12625000	Enhancers	Primary B cells from peripheral blood	blood
24	chr7:12624600-12625000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr7:12624600-12625000	Flanking Active TSS	A549	lung
26	chr7:12624600-12625000	Flanking Active TSS	Osteobl	bone
27	chr7:12624600-12625200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:12624800-12625000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:12624800-12625000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr7:12624800-12625000	Enhancers	NHDF-Ad	bronchial
31	chr7:12624800-12625600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr7:12624800-12625600	Enhancers	HSMM	muscle

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