Variant report

Variant	rs704979
Chromosome Location	chr3:42637664-42637665
allele	C/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	POLR2A	chr3:42637099-42637669	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:42636237-42639709	K562	blood:	n/a	n/a
3	POLR2A	chr3:42637601-42638153	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:42636950-42639278	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:42637462-42637868	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42631664..42634178-chr3:42636385..42639345,6	MCF-7	breast:
3	chr3:42603400..42605797-chr3:42635471..42638332,2	MCF-7	breast:
4	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2136012	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271181	0.86[EUR][1000 genomes]
rs2271185	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271186	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2976533	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339658	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339723	0.80[AMR][1000 genomes]
rs339725	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339726	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339727	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339728	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339733	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342521	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342522	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4549	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586082	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs587712	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597498	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607568	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612733	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614323	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617722	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627664	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs638836	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639692	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640689	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441892	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663673	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689251	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8351	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925457	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865109	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs704979	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs704979	NKTR	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
6	chr3:42633400-42641400	Weak transcription	Ovary	ovary
7	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
8	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
9	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
12	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
13	chr3:42633600-42638000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:42633600-42639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
19	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
21	chr3:42633600-42641200	Weak transcription	NHEK	skin
22	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
28	chr3:42633800-42638600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:42633800-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:42634000-42641600	Weak transcription	Lung	lung
33	chr3:42634200-42638800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
36	chr3:42634800-42638000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:42634800-42638200	Strong transcription	Fetal Thymus	thymus
38	chr3:42635000-42638600	Strong transcription	Primary B cells from cord blood	blood
39	chr3:42635000-42638600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr3:42635000-42639400	Strong transcription	HSMM	muscle
41	chr3:42635000-42639600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:42635200-42638600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:42635200-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:42635400-42638000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:42635400-42638200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:42635400-42638600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:42635400-42638600	Strong transcription	HMEC	breast
48	chr3:42635400-42641200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:42635400-42641200	Weak transcription	Brain Angular Gyrus	brain
50	chr3:42635600-42638600	Strong transcription	Primary T cells fromperipheralblood	blood

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