Variant report

Variant	rs968792
Chromosome Location	chr7:12624302-12624303
allele	C/T
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	RFX5	chr7:12624146-12624386	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12623803..12625558-chr7:12629908..12631864,2	K562	blood:
2	chr7:12623803..12627040-chr7:12629908..12631864,3	K562	blood:
3	chr7:12620852..12624352-chr7:12625661..12628427,3	K562	blood:

Variant related genes	Relation type
SCIN	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10233337	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10248988	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10255606	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]
rs10276226	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1129315	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17283514	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17283696	0.91[JPT][hapmap]
rs1859989	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859990	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990223	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990224	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1990225	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2215063	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240571	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240574	0.81[CEU][hapmap]
rs2240575	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3173628	0.85[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3735221	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3807863	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41379149	0.85[CEU][hapmap]
rs4361677	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460967	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460968	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6954578	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6972477	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73293093	0.86[ASN][1000 genomes]
rs7801351	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7811582	0.89[CEU][hapmap]

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
rs968792	SCIN	Cis_1M	lymphoblastoid	RTeQTL
rs968792	SCIN	cis	Thyroid	GTEx

Chromatin state (count:28 , 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	chr7:12620600-12624400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr7:12620600-12626600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:12620800-12624600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:12620800-12625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:12621800-12625600	Enhancers	Hela-S3	cervix
8	chr7:12622000-12624400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:12622000-12624600	Enhancers	Osteobl	bone
10	chr7:12622000-12625600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:12622600-12625000	Enhancers	Duodenum Mucosa	Duodenum
12	chr7:12622800-12624400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr7:12622800-12624400	Enhancers	K562	blood
14	chr7:12623000-12624400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:12623000-12624400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr7:12623000-12625200	Enhancers	Stomach Mucosa	stomach
17	chr7:12623200-12624600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:12623400-12624400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:12623400-12624600	Weak transcription	Gastric	stomach
20	chr7:12623400-12624600	Weak transcription	NHDF-Ad	bronchial
21	chr7:12623400-12624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:12623400-12628000	Weak transcription	Placenta	Placenta
23	chr7:12623600-12624600	Enhancers	A549	lung
24	chr7:12623800-12625200	Enhancers	Small Intestine	intestine
25	chr7:12624200-12624400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:12624200-12625200	Enhancers	HSMMtube	muscle
27	chr7:12624200-12625400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:12624200-12625600	Enhancers	Adipose Nuclei	Adipose

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