Variant report

Variant	rs654761
Chromosome Location	chr3:42656578-42656579
allele	A/C
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	chr3:42654292-42656698	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42655417..42657513-chr3:42690626..42693228,2	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13064311	0.93[ASN][1000 genomes]
rs13066173	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13066333	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs168138	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2068278	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2271184	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2271187	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2284305	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs237064	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2940407	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3095258	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339656	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339720	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339721	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339724	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339729	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339735	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342523	0.85[EUR][1000 genomes]
rs342535	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs342538	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs383937	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3888651	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs398743	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60994254	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612362	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs637852	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs638904	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651180	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663258	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs664813	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs665206	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs704982	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs807863	0.88[ASN][1000 genomes]
rs82755	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311323	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9311324	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813479	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9819563	0.92[ASN][1000 genomes]
rs9828279	0.91[AMR][1000 genomes];0.91[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	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
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs654761	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
8	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
11	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
12	chr3:42644800-42660200	Weak transcription	NH-A	brain
13	chr3:42645200-42660200	Weak transcription	HMEC	breast
14	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:42647000-42671400	Weak transcription	NHEK	skin
16	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:42647400-42672000	Weak transcription	NHLF	lung
19	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42647600-42677600	Weak transcription	Gastric	stomach
21	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
22	chr3:42649000-42657600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:42649400-42657000	Weak transcription	Primary B cells from cord blood	blood
24	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
25	chr3:42650200-42660000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:42650400-42657400	Weak transcription	Osteobl	bone
27	chr3:42650400-42658600	Weak transcription	HSMM	muscle
28	chr3:42650400-42659800	Weak transcription	Fetal Thymus	thymus
29	chr3:42650400-42660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:42650400-42660000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:42650400-42660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:42650400-42660600	Weak transcription	Fetal Heart	heart
33	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
34	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:42650600-42657000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:42650600-42657000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:42650600-42657400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:42650600-42658200	Weak transcription	Psoas Muscle	Psoas
40	chr3:42650600-42658200	Weak transcription	Right Atrium	heart
41	chr3:42650600-42660000	Weak transcription	Fetal Lung	lung
42	chr3:42650600-42660400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:42650600-42669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:42650600-42669400	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
47	chr3:42650800-42658200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:42650800-42660200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:42650800-42663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:42650800-42672800	Weak transcription	Ovary	ovary

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