Variant report

Variant	rs57615517
Chromosome Location	chr3:52322417-52322418
allele	A/G
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	GABPA	chr3:52321269-52322556	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:52320943-52322630	K562	blood:	n/a	n/a
3	ELF1	chr3:52321476-52322470	MCF-7	breast:	n/a	chr3:52321814-52321825 chr3:52322074-52322085 chr3:52321815-52321824
4	PML	chr3:52320769-52322545	GM12878	blood:	n/a	n/a
5	GABPA	chr3:52320890-52322432	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:52320771-52322817	GM19193	blood:	n/a	n/a
7	POLR2A	chr3:52320868-52322440	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:52320744-52322520	SK-N-MC	brain:	n/a	n/a
9	TAF1	chr3:52321372-52322450	ECC-1	luminal epithelium:	n/a	n/a
10	REST	chr3:52320925-52322600	H1-neurons	neurons:	n/a	chr3:52321828-52321841
11	POLR2A	chr3:52320558-52322521	U87	brain:	n/a	n/a
12	POLR2A	chr3:52320993-52322726	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr3:52320627-52322746	IMR90	lung:	n/a	n/a
14	JUN	chr3:52321488-52322418	K562	blood:	n/a	chr3:52322036-52322049 chr3:52322040-52322049
15	POLR2A	chr3:52320953-52322728	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:52320439-52322508	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:52321063-52322497	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:52320635-52323013	GM12878	blood:	n/a	n/a
19	HCFC1	chr3:52320857-52322792	Hela-S3	cervix:	n/a	n/a
20	ELF1	chr3:52321448-52322431	HCT-116	colon:	n/a	chr3:52321814-52321825 chr3:52322074-52322085 chr3:52321815-52321824
21	POLR2A	chr3:52320766-52322444	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:52320455-52322455	GM12878	blood:	n/a	n/a
23	GABPA	chr3:52321433-52322452	A549	lung:	n/a	n/a
24	ELF1	chr3:52321118-52322467	GM12878	blood:	n/a	chr3:52321814-52321825 chr3:52322074-52322085 chr3:52321815-52321824
25	GTF3C2	chr3:52321111-52322553	K562	blood:	n/a	n/a
26	JUND	chr3:52320711-52322489	SK-N-SH	brain:	n/a	chr3:52322040-52322049
27	POLR2A	chr3:52320120-52326729	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:52321217-52322461	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr3:52321255-52322427	Hela-S3	cervix:	n/a	n/a
30	YY1	chr3:52321346-52322496	SK-N-SH	brain:	n/a	chr3:52321788-52321799
31	POLR2A	chr3:52320558-52322570	U87	brain:	n/a	n/a
32	POLR2A	chr3:52320431-52322588	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:52320768-52322860	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:
2	chr3:52321086..52323733-chr3:52324166..52327461,5	MCF-7	breast:
3	chr11:62608856..62609653-chr3:52321247..52322510,4	Hela-S3	cervix:
4	chr1:91486993..91487505-chr3:52321844..52322675,2	HCT-116	colon:
5	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
6	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
7	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
8	chr3:52321744..52323842-chr3:52332822..52334732,2	MCF-7	breast:
9	chr3:52321768..52324071-chr3:52488633..52490328,2	K562	blood:
10	chr3:52187595..52189186-chr3:52321663..52323180,2	MCF-7	breast:
11	chr3:52278070..52281652-chr3:52320199..52323338,4	MCF-7	breast:
12	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
13	chr3:52271015..52274727-chr3:52321912..52324165,4	K562	blood:
14	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
15	chr10:75910494..75911172-chr3:52321735..52322598,2	NB4	blood:
16	chr3:52322040..52322619-chr6:86353056..86353783,2	Hela-S3	cervix:

Variant related genes	Relation type
GLYCTK	TF binding region
WDR82	TF binding region
ENSG00000168237	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000156110	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000242797	Chromatin interaction
ENSG00000122482	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000185009	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000239557	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1060330	0.86[ASN][1000 genomes]
rs11717383	0.85[ASN][1000 genomes]
rs13094687	0.82[AFR][1000 genomes]
rs1546737	0.90[EUR][1000 genomes]
rs2267847	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276834	0.84[ASN][1000 genomes]
rs34228726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34569561	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34656997	0.82[AFR][1000 genomes]
rs353547	0.85[ASN][1000 genomes]
rs3844291	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852063	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3852064	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57630131	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59565798	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445358	0.86[ASN][1000 genomes]
rs730050	0.80[ASN][1000 genomes]
rs7614727	0.86[ASN][1000 genomes]
rs7618915	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7622851	0.85[ASN][1000 genomes]
rs7629072	0.86[ASN][1000 genomes]
rs9311474	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57615517	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52320800-52322600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:52320800-52322600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:52320800-52322600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:52320800-52322600	Active TSS	HSMMtube	muscle
5	chr3:52320800-52322800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:52320800-52322800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:52320800-52322800	Active TSS	NHLF	lung
8	chr3:52321000-52322600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52321000-52322600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:52321000-52322600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:52321000-52323000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:52321200-52322600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52321200-52322600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52321200-52322600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:52321200-52322600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:52321200-52322600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52321200-52322600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52321200-52322600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52321200-52322600	Active TSS	Aorta	Aorta
20	chr3:52321200-52322600	Active TSS	Duodenum Mucosa	Duodenum
21	chr3:52321200-52322600	Active TSS	Lung	lung
22	chr3:52321200-52322600	Active TSS	Ovary	ovary
23	chr3:52321200-52322600	Active TSS	Psoas Muscle	Psoas
24	chr3:52321200-52322600	Active TSS	A549	lung
25	chr3:52321200-52322600	Active TSS	GM12878-XiMat	blood
26	chr3:52321200-52322600	Active TSS	HSMM	muscle
27	chr3:52321200-52322600	Active TSS	NHDF-Ad	bronchial
28	chr3:52321200-52322800	Active TSS	H1 Cell Line	embryonic stem cell
29	chr3:52321200-52322800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:52321200-52322800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:52321200-52322800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:52321200-52322800	Active TSS	K562	blood
33	chr3:52321200-52323000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:52321400-52322600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:52321400-52322600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52321400-52322600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52321400-52322600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:52321400-52322600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr3:52321400-52322600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:52321400-52322600	Active TSS	Primary T cells from cord blood	blood
41	chr3:52321400-52322600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:52321400-52322600	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr3:52321400-52322600	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr3:52321400-52322600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr3:52321400-52322600	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr3:52321400-52322600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:52321400-52322600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:52321400-52322600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52321400-52322600	Active TSS	Brain Angular Gyrus	brain
50	chr3:52321400-52322600	Active TSS	Brain Anterior Caudate	brain

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