Variant report

Variant	rs617722
Chromosome Location	chr3:42633498-42633499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
2	chr3:42632973..42636724-chr3:42645956..42649361,3	MCF-7	breast:
3	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
4	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

Variant related genes	Relation type
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000114857	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271181	0.85[EUR][1000 genomes]
rs2271185	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271186	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976533	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339658	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339723	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339725	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339726	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339727	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339728	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339733	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342521	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342522	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342536	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342537	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774398	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4549	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587712	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597498	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612733	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614323	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627664	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638836	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639692	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640689	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441892	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs663673	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689251	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8351	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925457	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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
rs617722	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs617722	NKTR	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42631600-42633800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:42631800-42633600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:42631800-42633600	Active TSS	Fetal Kidney	kidney
4	chr3:42632000-42633600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:42632200-42633600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:42632600-42633600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:42632600-42633600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:42632800-42633600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr3:42632800-42633600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:42632800-42633600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:42632800-42633600	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr3:42632800-42633600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr3:42632800-42633600	Flanking Active TSS	HUVEC	blood vessel
14	chr3:42632800-42633600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:42633000-42633600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
16	chr3:42633000-42633600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:42633000-42633600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:42633000-42633600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:42633000-42633600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:42633000-42633600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:42633000-42633600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:42633000-42633600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42633000-42633600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:42633000-42633600	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr3:42633000-42633600	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr3:42633000-42633600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:42633000-42633600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:42633000-42633600	Enhancers	Colon Smooth Muscle	Colon
29	chr3:42633000-42633600	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr3:42633000-42633600	Flanking Active TSS	Fetal Brain Female	brain
31	chr3:42633000-42633600	Enhancers	Fetal Heart	heart
32	chr3:42633000-42633600	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr3:42633000-42633600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr3:42633000-42633600	Flanking Active TSS	NH-A	brain
35	chr3:42633000-42633600	Flanking Active TSS	NHDF-Ad	bronchial
36	chr3:42633000-42633600	Flanking Active TSS	NHLF	lung
37	chr3:42633000-42633800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:42633000-42634600	Enhancers	Fetal Brain Male	brain
39	chr3:42633200-42633600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
40	chr3:42633200-42633600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:42633200-42633600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:42633200-42633600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:42633200-42633600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
44	chr3:42633200-42633600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:42633200-42633600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:42633200-42633600	Enhancers	Primary B cells from cord blood	blood
47	chr3:42633200-42633600	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr3:42633200-42633600	Enhancers	Primary T cells from cord blood	blood
49	chr3:42633200-42633600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
50	chr3:42633200-42633600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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