Variant report

Variant	rs614323
Chromosome Location	chr3:42625216-42625217
allele	G/T
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	JUN	chr3:42621793-42625488	K562	blood:	n/a	chr3:42622871-42622885

No.	Distal block	Cell Line	Cell type
1	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
2	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
3	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
4	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000114853	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000114857	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	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271181	0.83[EUR][1000 genomes]
rs2271185	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271186	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2976533	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339658	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339723	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs339725	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339726	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339727	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339728	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339733	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342521	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs342522	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4549	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs586082	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587712	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597498	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607568	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs612733	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs617722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627664	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638836	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639692	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs640689	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441892	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs663673	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689251	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704979	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8351	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs925457	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865109	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[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
rs614323	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs614323	NKTR	cis	Nerve Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624200-42631400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42624200-42631600	Weak transcription	HSMMtube	muscle
3	chr3:42624400-42625400	Enhancers	Fetal Thymus	thymus
4	chr3:42624400-42625400	Weak transcription	HMEC	breast
5	chr3:42624400-42625600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:42624400-42625600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:42624400-42629800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:42624400-42629800	Weak transcription	NHEK	skin
9	chr3:42624400-42631200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:42624400-42631200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:42624400-42631200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:42624400-42631400	Weak transcription	Liver	Liver
13	chr3:42624400-42631400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:42624400-42631400	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42624600-42625400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:42624600-42631200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:42624600-42631400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:42624600-42631400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:42624600-42631400	Weak transcription	Fetal Brain Male	brain
21	chr3:42624600-42631400	Weak transcription	A549	lung
22	chr3:42624800-42625400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:42624800-42625400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:42624800-42625400	Enhancers	K562	blood
25	chr3:42624800-42627000	Weak transcription	NHLF	lung
26	chr3:42624800-42630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:42624800-42631400	Weak transcription	Primary B cells from cord blood	blood
28	chr3:42624800-42631400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:42624800-42631400	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:42624800-42631400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:42624800-42631400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:42624800-42631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:42624800-42631600	Weak transcription	Gastric	stomach
34	chr3:42625000-42630200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:42625000-42631000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:42625000-42631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:42625000-42631200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:42625000-42631200	Weak transcription	GM12878-XiMat	blood
39	chr3:42625000-42631400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:42625000-42631400	Weak transcription	Brain Germinal Matrix	brain
41	chr3:42625000-42631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:42625000-42631400	Weak transcription	Fetal Intestine Small	intestine
43	chr3:42625000-42631600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:42625200-42625400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:42625200-42625400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:42625200-42625600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr3:42625200-42625600	Enhancers	Dnd41	blood
48	chr3:42625200-42631400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:42625200-42631600	Weak transcription	H9 Cell Line	embryonic stem cell

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