Variant report

Variant	rs4687689
Chromosome Location	chr3:52948674-52948675
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52947000..52950215-chr3:52950921..52954800,3	K562	blood:
2	chr3:52947000..52951038-chr3:52951338..52956335,5	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10865977	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130331	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715347	0.81[EUR][1000 genomes]
rs11915546	0.80[EUR][1000 genomes]
rs11922975	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12487379	0.88[EUR][1000 genomes]
rs12492391	0.93[EUR][1000 genomes]
rs12629687	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12638968	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13072537	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336558	0.81[EUR][1000 genomes]
rs2336664	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336667	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2336668	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2710314	0.80[AFR][1000 genomes]
rs3821873	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4350911	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687562	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4687679	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4687680	0.94[EUR][1000 genomes]
rs4687682	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687683	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687684	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687687	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019197	0.80[EUR][1000 genomes]
rs56383738	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253583	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6764322	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6769789	0.81[EUR][1000 genomes]
rs6773650	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6795646	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7612624	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7620690	0.83[EUR][1000 genomes]
rs7626551	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7630552	0.83[EUR][1000 genomes]
rs9810807	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9825230	0.92[EUR][1000 genomes]
rs9836499	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850563	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9860296	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9865248	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866243	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871175	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880619	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880978	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9985365	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	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
2	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4687689	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs4687689	ITIH4-AS1	cis	Artery Tibial	GTEx
rs4687689	ITIH4-AS1	cis	Artery Aorta	GTEx
rs4687689	ITIH4-AS1	cis	lung	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
4	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52932200-52948800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:52932200-52951400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:52932200-52952800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:52932200-52953600	Weak transcription	Right Ventricle	heart
11	chr3:52932200-52953800	Weak transcription	Ovary	ovary
12	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
13	chr3:52932200-52961800	Weak transcription	A549	lung
14	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
15	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52932200-52967800	Weak transcription	HSMM	muscle
17	chr3:52932200-52968600	Weak transcription	Osteobl	bone
18	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
20	chr3:52932400-52953000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:52932400-52953400	Weak transcription	Fetal Kidney	kidney
22	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
24	chr3:52932400-52968800	Weak transcription	NHEK	skin
25	chr3:52935600-52968600	Strong transcription	Dnd41	blood
26	chr3:52937200-52959800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52938000-52959000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:52939400-52953000	Weak transcription	Aorta	Aorta
29	chr3:52939600-52953400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52939600-52961200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:52940200-52949000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52940200-52953400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:52941000-52949200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:52941200-52949000	Weak transcription	HMEC	breast
35	chr3:52941400-52952000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:52941800-52961600	Weak transcription	Colonic Mucosa	Colon
37	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
38	chr3:52942000-52948800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:52943000-52950600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:52943200-52950400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:52943200-52950400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52943200-52958800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:52943200-52958800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:52943600-52950000	Strong transcription	Fetal Intestine Large	intestine
45	chr3:52943600-52950200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:52943600-52950400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:52943600-52950400	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52943600-52950400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:52943600-52957000	Strong transcription	Placenta	Placenta
50	chr3:52943600-52962400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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