Variant report

Variant	rs6414570
Chromosome Location	chr3:52788959-52788960
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	chr3:52787616..52789879-chr3:52803393..52805587,2	MCF-7	breast:
2	chr3:52788031..52789791-chr3:52792352..52793907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1014969	0.84[EUR][1000 genomes]
rs1029871	0.85[EUR][1000 genomes]
rs10865974	0.83[AMR][1000 genomes]
rs11130321	0.81[AMR][1000 genomes]
rs11130323	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130325	0.81[EUR][1000 genomes]
rs11130327	0.85[EUR][1000 genomes]
rs11714030	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11716747	0.83[AMR][1000 genomes]
rs11717836	0.83[EUR][1000 genomes]
rs12497998	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635140	0.83[AMR][1000 genomes]
rs13061423	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13071584	0.87[EUR][1000 genomes]
rs13074853	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13079063	0.83[AMR][1000 genomes]
rs13082208	0.81[EUR][1000 genomes]
rs13082960	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13095332	0.84[EUR][1000 genomes]
rs1468638	0.83[AMR][1000 genomes]
rs1866268	0.82[AMR][1000 genomes]
rs2072390	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2079929	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2109634	0.84[AMR][1000 genomes]
rs2159644	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2164885	0.83[AMR][1000 genomes]
rs2230534	0.85[EUR][1000 genomes]
rs2230535	0.85[EUR][1000 genomes]
rs2268024	0.83[EUR][1000 genomes]
rs2268025	0.85[EUR][1000 genomes]
rs2268026	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2286800	0.80[EUR][1000 genomes]
rs2289247	0.82[AMR][1000 genomes]
rs2336545	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34157897	0.82[AMR][1000 genomes]
rs34291015	0.81[ASN][1000 genomes]
rs34739010	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34918356	0.81[AMR][1000 genomes]
rs35315313	0.83[AMR][1000 genomes]
rs35526119	0.83[AMR][1000 genomes]
rs3733039	0.83[AMR][1000 genomes]
rs3733041	0.83[AMR][1000 genomes]
rs3755798	0.83[AMR][1000 genomes]
rs4435633	0.80[AMR][1000 genomes]
rs4687644	0.83[AMR][1000 genomes]
rs4687648	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4687650	0.83[EUR][1000 genomes]
rs62255396	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6414569	0.80[AMR][1000 genomes]
rs6445531	0.82[AMR][1000 genomes]
rs6445534	0.83[AMR][1000 genomes]
rs6445535	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6617	0.83[AMR][1000 genomes]
rs6787154	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7624716	0.83[AMR][1000 genomes]
rs7638162	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7653028	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs767418	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs998909	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6414570	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs6414570	MUSTN1	cis	Artery Aorta	GTEx
rs6414570	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs6414570	NT5DC2	cis	lung	GTEx
rs6414570	PBRM1	cis	Thyroid	GTEx
rs6414570	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs6414570	PBRM1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
9	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
10	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
14	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
16	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
19	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:52768000-52789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:52770200-52789000	Strong transcription	Fetal Stomach	stomach
25	chr3:52770200-52797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:52770800-52789400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:52771200-52789400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:52771200-52800800	Strong transcription	Fetal Lung	lung
29	chr3:52772600-52794800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:52774000-52803400	Weak transcription	K562	blood
31	chr3:52774400-52789200	Strong transcription	Fetal Intestine Small	intestine
32	chr3:52775200-52800600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:52775200-52802600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:52775400-52789000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:52775600-52789400	Strong transcription	Primary T cells from cord blood	blood
36	chr3:52775800-52789400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:52775800-52802800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:52775800-52802800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:52776000-52794200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr3:52778400-52802400	Strong transcription	Liver	Liver
41	chr3:52779400-52793800	Weak transcription	NHLF	lung
42	chr3:52781000-52792800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:52781000-52796000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:52781000-52799000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:52781200-52791800	Weak transcription	HSMMtube	muscle
46	chr3:52782400-52789400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr3:52782600-52801000	Strong transcription	Dnd41	blood
48	chr3:52783200-52791000	Weak transcription	HSMM	muscle
49	chr3:52783200-52803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:52784600-52789000	Strong transcription	Ovary	ovary

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