Variant report

Variant	rs7629072
Chromosome Location	chr3:52305633-52305634
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	chr3:52305520-52305670	GM12864	blood:	n/a	n/a
2	POLR2A	chr3:52305416-52305814	GM12878	blood:	n/a	n/a
3	SMC3	chr3:52305582-52305847	GM12878	blood:	n/a	n/a
4	CTCF	chr3:52305600-52305750	A549	lung:	n/a	n/a
5	BHLHE40	chr3:52305032-52305765	GM12878	blood:	n/a	n/a
6	ZNF384	chr3:52305414-52305828	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52304087..52306795-chr3:52318600..52320906,2	K562	blood:
2	chr3:52292200..52293754-chr3:52305089..52307890,2	MCF-7	breast:
3	chr3:52304279..52306605-chr3:52344812..52346956,2	K562	blood:
4	chr3:52304494..52307260-chr3:52321098..52323365,4	K562	blood:

Variant related genes	Relation type
WDR82	TF binding region
MIRLET7G	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1060330	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705963	0.83[AFR][1000 genomes]
rs11706108	0.83[AFR][1000 genomes]
rs11717383	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091545	0.83[AFR][1000 genomes]
rs2276834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34228726	0.86[ASN][1000 genomes]
rs34569561	0.85[ASN][1000 genomes]
rs353547	0.88[ASN][1000 genomes]
rs35860312	0.81[AFR][1000 genomes]
rs3844291	0.83[ASN][1000 genomes]
rs3852063	0.86[ASN][1000 genomes]
rs3852064	0.85[ASN][1000 genomes]
rs498946	0.81[YRI][hapmap]
rs57615517	0.86[ASN][1000 genomes]
rs57630131	0.82[ASN][1000 genomes]
rs59565798	0.87[ASN][1000 genomes]
rs610060	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66462821	0.81[AFR][1000 genomes]
rs6794675	0.83[AFR][1000 genomes]
rs730050	0.93[ASN][1000 genomes]
rs7614727	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618915	0.85[ASN][1000 genomes]
rs7622851	0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643570	0.83[AFR][1000 genomes]
rs9311474	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7629072	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:52283000-52306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:52284600-52305800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:52285600-52308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:52285800-52307400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr3:52286400-52306800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:52288000-52305800	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:52292400-52309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52292800-52305800	Strong transcription	Fetal Intestine Large	intestine
15	chr3:52293000-52308000	Weak transcription	Stomach Mucosa	stomach
16	chr3:52293800-52306200	Strong transcription	NH-A	brain
17	chr3:52293800-52307200	Strong transcription	HSMM	muscle
18	chr3:52297400-52311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:52300000-52310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:52300000-52310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52300200-52310200	Weak transcription	HSMMtube	muscle
22	chr3:52300600-52310800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52301200-52311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:52301800-52307200	Genic enhancers	Adipose Nuclei	Adipose
25	chr3:52302600-52306800	Weak transcription	A549	lung
26	chr3:52302600-52307800	Weak transcription	Pancreas	Pancrea
27	chr3:52302600-52310000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:52302800-52310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:52303000-52311200	Weak transcription	Esophagus	oesophagus
30	chr3:52303400-52305800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:52303400-52306200	Genic enhancers	Brain Hippocampus Middle	brain
32	chr3:52303400-52310000	Weak transcription	Aorta	Aorta
33	chr3:52303600-52305800	Weak transcription	Lung	lung
34	chr3:52303600-52306200	Weak transcription	Spleen	Spleen
35	chr3:52303600-52306200	Enhancers	HUVEC	blood vessel
36	chr3:52303600-52307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:52303600-52308400	Strong transcription	NHEK	skin
38	chr3:52303600-52309600	Genic enhancers	Primary B cells from cord blood	blood
39	chr3:52303800-52306000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52303800-52307000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52303800-52307400	Genic enhancers	Liver	Liver
42	chr3:52303800-52308200	Weak transcription	Gastric	stomach
43	chr3:52303800-52309600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:52304000-52306000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:52304000-52306000	Enhancers	Colon Smooth Muscle	Colon
46	chr3:52304000-52306000	Enhancers	Right Atrium	heart
47	chr3:52304000-52306400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:52304000-52306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:52304000-52307000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:52304000-52311000	Genic enhancers	Primary B cells from peripheral blood	blood

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