Variant report

Variant	rs12141995
Chromosome Location	chr1:223603809-223603810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223597589..223600437-chr1:223603071..223605858,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10494039	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495206	0.84[ASW][hapmap]
rs1115114	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590684	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12134824	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1400959	0.84[ASW][hapmap]
rs17162072	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17480087	1.00[ASW][hapmap]
rs17480344	0.84[ASW][hapmap]
rs17539269	1.00[ASW][hapmap]
rs17539583	0.84[ASW][hapmap]
rs17577742	1.00[ASW][hapmap]
rs17578168	0.84[ASW][hapmap]
rs17578203	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs61839881	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7526539	0.88[AMR][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	nsv832670	chr1:223561771-223683381	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv4687	chr1:223565080-223610362	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv873208	chr1:223603809-223639469	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141995	SUSD4	cis	cerebellum	SCAN
rs12141995	SUSD4	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223595200-223609200	Weak transcription	Right Atrium	heart
2	chr1:223599400-223604600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:223601800-223605000	Enhancers	Colon Smooth Muscle	Colon
4	chr1:223602000-223604400	Enhancers	Fetal Heart	heart
5	chr1:223602000-223604400	Enhancers	Rectal Smooth Muscle	rectum
6	chr1:223602200-223604200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223602200-223604200	Enhancers	NHEK	skin
8	chr1:223602200-223604400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr1:223602200-223604600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:223602200-223604600	Enhancers	Stomach Smooth Muscle	stomach
11	chr1:223602400-223604200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:223602400-223604200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:223602400-223604200	Enhancers	NHDF-Ad	bronchial
14	chr1:223602400-223604400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:223602400-223604400	Enhancers	HMEC	breast
16	chr1:223602400-223604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:223602600-223604000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr1:223602600-223604000	Enhancers	Gastric	stomach
19	chr1:223602600-223604000	Enhancers	Stomach Mucosa	stomach
20	chr1:223602600-223604200	Enhancers	Pancreas	Pancrea
21	chr1:223602600-223604400	Enhancers	Osteobl	bone
22	chr1:223603000-223604400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:223603000-223609000	Weak transcription	Left Ventricle	heart
24	chr1:223603400-223605400	Enhancers	Esophagus	oesophagus
25	chr1:223603600-223604200	Enhancers	Ovary	ovary
26	chr1:223603600-223604400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:223603800-223604400	Enhancers	Aorta	Aorta
28	chr1:223603800-223604400	Enhancers	Fetal Stomach	stomach
29	chr1:223603800-223609000	Weak transcription	Right Ventricle	heart

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