Variant report

Variant	rs12093839
Chromosome Location	chr1:184405359-184405360
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	chr1:184355831..184357854-chr1:184403714..184405502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction
ENSG00000271387	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10157833	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10158710	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489721	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10489722	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10494580	0.94[CEU][hapmap]
rs10752935	0.93[CHB][hapmap]
rs10797966	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10911592	0.94[CEU][hapmap]
rs10911593	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11802306	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11805001	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11810399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11811039	0.86[ASN][1000 genomes]
rs12029316	0.94[CEU][hapmap]
rs12048492	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs12057850	0.91[ASN][1000 genomes]
rs12058294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12063210	0.85[ASN][1000 genomes]
rs12070787	0.89[EUR][1000 genomes]
rs1535135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16823149	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1969686	0.91[ASN][1000 genomes]
rs2207522	0.95[ASN][1000 genomes]
rs3916684	0.86[ASN][1000 genomes]
rs3930803	0.91[ASN][1000 genomes]
rs4233119	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs4512607	0.94[CEU][hapmap]
rs4518858	0.93[CHB][hapmap]
rs57024489	0.85[ASN][1000 genomes]
rs57790643	0.85[ASN][1000 genomes]
rs58462114	0.89[ASN][1000 genomes]
rs59369289	0.85[ASN][1000 genomes]
rs61823506	0.89[ASN][1000 genomes]
rs61823538	0.89[ASN][1000 genomes]
rs61823539	0.89[ASN][1000 genomes]
rs61823542	0.91[ASN][1000 genomes]
rs61823543	0.99[ASN][1000 genomes]
rs61823546	0.85[ASN][1000 genomes]
rs6424948	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs6424949	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs6656089	0.85[ASN][1000 genomes]
rs6657105	0.87[ASN][1000 genomes]
rs6657254	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6666696	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6696161	0.93[CHB][hapmap];0.84[CHD][hapmap]
rs72735678	0.91[ASN][1000 genomes]
rs7367466	0.94[CEU][hapmap]
rs7522628	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7537725	0.95[ASN][1000 genomes]
rs7540361	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12093839	NPL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184383800-184412400	Weak transcription	Fetal Stomach	stomach
2	chr1:184390600-184422400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:184392200-184408200	Weak transcription	Esophagus	oesophagus
4	chr1:184395000-184405600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:184395400-184408000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:184395800-184405600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:184396000-184412800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:184396200-184412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:184396200-184418800	Weak transcription	NHEK	skin
10	chr1:184396200-184419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:184396400-184430000	Weak transcription	Spleen	Spleen
12	chr1:184398400-184410200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:184398600-184411400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:184398800-184418800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:184400400-184412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:184402200-184405600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:184402400-184406600	Weak transcription	Pancreas	Pancrea
18	chr1:184402600-184417400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:184403000-184423600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:184403400-184409800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:184403600-184405400	Weak transcription	Stomach Mucosa	stomach
22	chr1:184403800-184406400	Weak transcription	Right Atrium	heart
23	chr1:184403800-184411400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:184404200-184407400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:184404600-184405800	Enhancers	Lung	lung
26	chr1:184404600-184406200	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:184404800-184406000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:184404800-184412800	Weak transcription	Left Ventricle	heart
29	chr1:184405000-184407000	Enhancers	Fetal Intestine Large	intestine
30	chr1:184405000-184407800	Enhancers	Psoas Muscle	Psoas
31	chr1:184405200-184405600	Weak transcription	Right Ventricle	heart
32	chr1:184405200-184407800	Enhancers	Rectal Mucosa Donor 31	rectum

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