Variant report

Variant	rs2303793
Chromosome Location	chr16:70530359-70530360
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	CTCF	chr16:70530280-70530430	GM12875	blood:	n/a	n/a
2	CTCF	chr16:70530280-70530430	GM12864	blood:	n/a	n/a
3	CTCF	chr16:70530300-70530450	A549	lung:	n/a	n/a
4	CTCF	chr16:70530308-70530427	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr16:70530280-70530430	K562	blood:	n/a	n/a
6	CTCF	chr16:70530300-70530450	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr16:70530260-70530410	MCF-7	breast:	n/a	n/a
8	CTCF	chr16:70530300-70530450	GM12868	blood:	n/a	n/a
9	CTCF	chr16:70530340-70530490	GM12873	blood:	n/a	n/a
10	CTCF	chr16:70530340-70530490	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr16:70530320-70530470	HEK293	kidney:	n/a	n/a
12	CTCF	chr16:70530340-70530490	GM12864	blood:	n/a	n/a
13	CTCF	chr16:70530300-70530450	GM12871	blood:	n/a	n/a
14	CTCF	chr16:70530240-70530390	MCF-7	breast:	n/a	n/a
15	POLR2A	chr16:70530262-70530413	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70528428..70531300-chr16:70556164..70557770,2	MCF-7	breast:

Variant related genes	Relation type
COG4	TF binding region
ENSG00000103051	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10852465	0.80[ASN][1000 genomes]
rs11075767	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075768	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075769	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11075770	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11640374	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs11641683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643344	0.88[ASN][1000 genomes]
rs11643373	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11643823	0.80[EUR][1000 genomes]
rs11645092	0.80[EUR][1000 genomes]
rs11645214	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11645287	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs11645437	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11645585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648402	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11649624	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11865527	0.88[ASN][1000 genomes]
rs11866400	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12447090	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12597401	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12925729	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12933634	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168606	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2288491	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303791	0.83[AMR][1000 genomes]
rs2303792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs33910368	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34567847	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34890962	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3852695	0.93[YRI][hapmap]
rs3859068	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4277334	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4284632	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4324119	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4436771	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4592653	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs58963621	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499317	0.82[AMR][1000 genomes]
rs6499320	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499321	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499327	0.83[YRI][hapmap]
rs71401814	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189474	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7192268	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7194521	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7195030	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7197262	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7197840	0.84[EUR][1000 genomes]
rs7198317	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7199859	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201750	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7204583	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs722579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744672	0.85[ASN][1000 genomes]
rs7919	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs8045651	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046881	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8047409	0.81[AMR][1000 genomes]
rs8049641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049786	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051506	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8052031	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8052125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053436	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8057610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8057766	0.93[YRI][hapmap]
rs8058224	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8062178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8062183	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8063990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891138	0.81[YRI][hapmap]
rs936994	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9635522	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9921696	0.93[YRI][hapmap]
rs9925510	0.96[YRI][hapmap]
rs9929904	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934440	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9936225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2303793	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs2303793	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2303793	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs2303793	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs2303793	RP11-296I10.6	cis	Thyroid	GTEx
rs2303793	IL34	cis	Nerve Tibial	GTEx
rs2303793	CLEC18A	cis	Artery Aorta	GTEx
rs2303793	RP11-296I10.6	cis	Artery Tibial	GTEx
rs2303793	CLEC18A	cis	Whole Blood	GTEx
rs2303793	LOC283970	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70501200-70535800	Strong transcription	Fetal Intestine Small	intestine
3	chr16:70501400-70535200	Strong transcription	Fetal Intestine Large	intestine
4	chr16:70501400-70536400	Strong transcription	Fetal Stomach	stomach
5	chr16:70504200-70532000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr16:70504400-70535200	Strong transcription	Liver	Liver
7	chr16:70506400-70535200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:70506600-70535400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr16:70511800-70535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:70512000-70535400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr16:70512800-70533600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:70513800-70532200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr16:70517600-70538800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr16:70518000-70545800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:70519800-70532200	Strong transcription	Primary T cells from cord blood	blood
17	chr16:70519800-70533400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr16:70522200-70532000	Strong transcription	Fetal Lung	lung
19	chr16:70522800-70531800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:70522800-70532200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr16:70523200-70535200	Strong transcription	Brain Germinal Matrix	brain
22	chr16:70523200-70542400	Weak transcription	Hela-S3	cervix
23	chr16:70523400-70535200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr16:70523400-70535200	Strong transcription	Dnd41	blood
25	chr16:70524000-70532200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr16:70524400-70542400	Weak transcription	Fetal Brain Male	brain
27	chr16:70524600-70532000	Strong transcription	Lung	lung
28	chr16:70524600-70535200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr16:70525200-70535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:70525400-70535800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr16:70525600-70532000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr16:70525600-70533400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr16:70525600-70534000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:70525600-70535400	Strong transcription	Fetal Muscle Leg	muscle
35	chr16:70525600-70535800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr16:70525600-70538200	Strong transcription	Fetal Thymus	thymus
37	chr16:70525800-70533200	Strong transcription	Osteobl	bone
38	chr16:70525800-70533400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr16:70525800-70533800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:70525800-70535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:70525800-70535200	Strong transcription	Adipose Nuclei	Adipose
42	chr16:70525800-70535600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:70525800-70535600	Strong transcription	Placenta	Placenta
44	chr16:70525800-70535800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:70525800-70537000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:70526000-70539000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr16:70526600-70532000	Strong transcription	Brain Hippocampus Middle	brain
48	chr16:70526600-70532000	Strong transcription	Esophagus	oesophagus
49	chr16:70526600-70532000	Strong transcription	Spleen	Spleen
50	chr16:70526600-70533400	Strong transcription	Ovary	ovary

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