Variant report

Variant	rs2146901
Chromosome Location	chr1:172119559-172119560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172114639..172117543-chr1:172117607..172120253,2	K562	blood:
2	chr1:172109737..172112011-chr1:172117848..172120682,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10442603	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10797791	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911101	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10911109	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10911110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911111	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911112	1.00[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs10911116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911121	0.94[CEU][hapmap]
rs10911124	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10911125	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12047492	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12117047	0.91[ASN][1000 genomes]
rs12120556	1.00[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs12139213	0.99[ASN][1000 genomes]
rs12141278	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475230	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1475231	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2181624	1.00[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs2421986	0.94[EUR][1000 genomes]
rs2421987	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35419194	0.91[ASN][1000 genomes]
rs4604727	0.94[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs56848769	0.92[ASN][1000 genomes]
rs57543724	0.91[ASN][1000 genomes]
rs59123063	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61046549	0.92[ASN][1000 genomes]
rs72719075	0.88[EUR][1000 genomes]
rs72719086	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7519823	0.95[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2146901	TNFSF4	cis	parietal	SCAN
rs2146901	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172114400-172137000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172114800-172123600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:172115000-172119600	Weak transcription	Ovary	ovary
4	chr1:172115000-172119800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:172115000-172123400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:172115000-172123600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:172115000-172133800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:172115600-172132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:172116000-172123400	Weak transcription	NH-A	brain
10	chr1:172116400-172123200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:172116800-172123400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:172117600-172120000	Enhancers	Fetal Stomach	stomach
13	chr1:172117800-172122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:172118000-172119600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:172118000-172122200	Weak transcription	HMEC	breast
16	chr1:172118200-172122400	Weak transcription	NHLF	lung
17	chr1:172118200-172123200	Weak transcription	HUVEC	blood vessel
18	chr1:172118800-172119600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:172118800-172122200	Weak transcription	NHDF-Ad	bronchial
20	chr1:172118800-172122200	Weak transcription	NHEK	skin
21	chr1:172119000-172119800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:172119000-172122400	Weak transcription	Osteobl	bone
23	chr1:172119000-172125000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:172119200-172120000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:172119200-172120400	Weak transcription	Fetal Kidney	kidney
26	chr1:172119200-172122000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:172119200-172122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:172119400-172119600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:172119400-172119600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:172119400-172121800	Weak transcription	Fetal Lung	lung

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