Variant report

Variant	rs597498
Chromosome Location	chr3:42635384-42635385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42632973..42636724-chr3:42645956..42649361,3	MCF-7	breast:
2	chr3:42635009..42637446-chr3:42638784..42643768,7	MCF-7	breast:
3	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2136012	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271181	0.86[EUR][1000 genomes]
rs2271185	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271186	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2976533	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339658	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339723	0.82[AMR][1000 genomes]
rs339725	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339726	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339728	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339733	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342521	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342522	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342536	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342537	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774398	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4549	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612733	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614323	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617722	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627664	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs638836	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639692	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640689	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441892	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663673	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689251	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704979	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8351	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs925457	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9865109	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs597498	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs597498	NKTR	cis	Nerve Tibial	GTEx
rs597498	NKTR	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42635600	Genic enhancers	Primary T cells fromperipheralblood	blood
2	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
3	chr3:42633200-42641600	Weak transcription	Gastric	stomach
4	chr3:42633400-42635400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:42633400-42635400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:42633400-42635400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:42633400-42636400	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
11	chr3:42633400-42641400	Weak transcription	Ovary	ovary
12	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
13	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
14	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
17	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
18	chr3:42633600-42635400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:42633600-42635400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:42633600-42635400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:42633600-42635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:42633600-42635400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:42633600-42635400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:42633600-42635400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:42633600-42635400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:42633600-42635400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:42633600-42635400	Weak transcription	NHLF	lung
28	chr3:42633600-42635400	Weak transcription	Osteobl	bone
29	chr3:42633600-42635600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:42633600-42635600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:42633600-42635600	Strong transcription	Hela-S3	cervix
32	chr3:42633600-42635800	Genic enhancers	Dnd41	blood
33	chr3:42633600-42636000	Weak transcription	Primary T cells from cord blood	blood
34	chr3:42633600-42636400	Strong transcription	Fetal Lung	lung
35	chr3:42633600-42636800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:42633600-42637000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:42633600-42637600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:42633600-42638000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:42633600-42639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
44	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
46	chr3:42633600-42641200	Weak transcription	NHEK	skin
47	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
50	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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