Variant report

Variant	rs3890789
Chromosome Location	chr2:114514391-114514392
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	E2F6	chr2:114514188-114514458	K562	blood:	n/a	chr2:114514302-114514311 chr2:114514300-114514309
2	E2F6	chr2:114514074-114514577	A549	lung:	n/a	chr2:114514302-114514311 chr2:114514300-114514309
3	POLR2A	chr2:114513704-114514574	A549	lung:	n/a	n/a
4	E2F6	chr2:114514163-114514416	K562	blood:	n/a	chr2:114514302-114514311 chr2:114514300-114514309
5	ETS1	chr2:114513659-114514596	K562	blood:	n/a	chr2:114514281-114514291
6	MBD4	chr2:114513652-114514993	HepG2	liver:	n/a	n/a
7	RAD21	chr2:114514160-114514661	GM12878	blood:	n/a	n/a
8	RAD21	chr2:114514294-114514458	K562	blood:	n/a	n/a
9	POLR2A	chr2:114513244-114515044	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:114513138-114515445	K562	blood:	n/a	n/a
11	POLR2A	chr2:114513272-114515179	Hela-S3	cervix:	n/a	n/a
12	NRF1	chr2:114514183-114514499	GM12878	blood:	n/a	n/a
13	HCFC1	chr2:114513778-114514934	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:114513777-114515323	SK-N-MC	brain:	n/a	n/a
15	PML	chr2:114513843-114514818	K562	blood:	n/a	n/a
16	POLR2A	chr2:114513706-114514559	A549	lung:	n/a	n/a
17	CTCF	chr2:114514363-114514406	Spleen_OC	spleen:	n/a	n/a
18	ATF2	chr2:114514125-114514475	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF7	chr2:114513777-114514593	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:114513379-114514909	GM19099	blood:	n/a	n/a
21	RCOR1	chr2:114513285-114514772	K562	blood:	n/a	n/a
22	TBP	chr2:114513588-114514741	H1-hESC	embryonic stem cell:	n/a	n/a
23	EP300	chr2:114513989-114514694	A549	lung:	n/a	n/a
24	POLR2A	chr2:114513623-114514766	K562	blood:	n/a	n/a
25	ZNF384	chr2:114513824-114514560	GM12878	blood:	n/a	n/a
26	RUNX3	chr2:114513678-114514889	GM12878	blood:	n/a	n/a
27	TAL1	chr2:114513833-114514808	K562	blood:	n/a	n/a
28	YY1	chr2:114513688-114514471	SK-N-SH_RA	brain:	n/a	chr2:114513769-114513783
29	BHLHE40	chr2:114513749-114514736	K562	blood:	n/a	n/a
30	MAFK	chr2:114514211-114514741	K562	blood:	n/a	n/a
31	ELF1	chr2:114514050-114514538	A549	lung:	n/a	chr2:114514280-114514289 chr2:114514276-114514289
32	GABPA	chr2:114514060-114514660	A549	lung:	n/a	chr2:114514529-114514538
33	ZBTB33	chr2:114514215-114514469	HepG2	liver:	n/a	n/a
34	ATF3	chr2:114514146-114514474	K562	blood:	n/a	chr2:114514298-114514313 chr2:114514300-114514311 chr2:114514302-114514309 chr2:114514302-114514312 chr2:114514299-114514312 chr2:114514300-114514313 chr2:114514302-114514312 chr2:114514290-114514310 chr2:114514301-114514309 chr2:114514299-114514310 chr2:114514301-114514321 chr2:114514298-114514309 chr2:114514302-114514310 chr2:114514301-114514312 chr2:114514299-114514312
35	MXI1	chr2:114513683-114514800	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF12	chr2:114513713-114514704	ECC-1	luminal epithelium:	n/a	chr2:114513865-114513875
37	SP1	chr2:114513757-114514655	A549	lung:	n/a	chr2:114513802-114513816
38	ATF2	chr2:114514093-114514525	H1-hESC	embryonic stem cell:	n/a	n/a
39	JUND	chr2:114513973-114514597	A549	lung:	n/a	chr2:114514301-114514310
40	MXI1	chr2:114512572-114514844	IMR90	lung:	n/a	n/a
41	RELA	chr2:114513930-114514832	GM15510	blood:	n/a	n/a
42	POU2F2	chr2:114514238-114514489	GM12878	blood:	n/a	n/a
43	REST	chr2:114513936-114514487	PFSK-1	brain:	n/a	n/a
44	RAD21	chr2:114513998-114514611	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr2:114513533-114514908	HepG2	liver:	n/a	n/a
46	SRF	chr2:114514096-114514431	H1-hESC	embryonic stem cell:	n/a	n/a
47	CUX1	chr2:114514307-114514858	GM12878	blood:	n/a	n/a
48	GABPA	chr2:114513852-114514474	HepG2	liver:	n/a	n/a
49	POU2F2	chr2:114514158-114514667	GM12891	blood:	n/a	n/a
50	HA-E2F1	chr2:114513768-114514559	Hela-S3	cervix:	n/a	chr2:114514302-114514311 chr2:114514300-114514309

No.	Distal block	Cell Line	Cell type
1	chr2:114512789..114515409-chr20:55840179..55841852,2	MCF-7	breast:
2	chr2:114512629..114516386-chr2:114645660..114650521,15	K562	blood:
3	chr2:114491572..114494215-chr2:114513189..114515373,3	K562	blood:
4	chr2:114513011..114515179-chr2:114599381..114601639,2	MCF-7	breast:
5	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
6	chr2:114514046..114514656-chr5:122758831..122759348,2	HCT-116	colon:
7	chr2:114512680..114516386-chr2:114646106..114650521,15	K562	blood:
8	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
9	chr2:114513771..114515245-chr2:114647371..114648721,7	MCF-7	breast:
10	chr2:114512943..114515625-chr2:114589095..114591354,2	MCF-7	breast:
11	chr11:62312627..62313318-chr2:114514037..114514594,2	Hela-S3	cervix:
12	chr2:114489220..114494215-chr2:114513189..114517576,5	K562	blood:
13	chr2:114501133..114502988-chr2:114513074..114515544,2	K562	blood:

Variant related genes	Relation type
SLC35F5	TF binding region
ENSG00000101144	Chromatin interaction
ENSG00000168944	Chromatin interaction
ENSG00000228857	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000270019	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10167730	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10172842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177576	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179657	0.92[EUR][1000 genomes]
rs10209098	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12711788	0.81[EUR][1000 genomes]
rs1375332	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2122097	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2290108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442136	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595152	0.94[CEU][hapmap]
rs2687627	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28451366	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2900744	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36062527	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3816384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848343	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4848345	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849277	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4849279	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6711542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7560480	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7577893	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600228	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3890789	RPL23AP7	cis	Artery Tibial	GTEx
rs3890789	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs3890789	DDX11L2	cis	Whole Blood	GTEx
rs3890789	RPL23AP7	cis	Nerve Tibial	GTEx
rs3890789	RPL23AP7	cis	Muscle Skeletal	GTEx
rs3890789	RPL23AP7	cis	Whole Blood	GTEx
rs3890789	RPL23AP7	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114511200-114515000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:114511600-114515200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:114512000-114514600	Active TSS	HSMMtube	muscle
4	chr2:114512000-114514800	Active TSS	HMEC	breast
5	chr2:114512000-114515200	Active TSS	NHDF-Ad	bronchial
6	chr2:114512000-114515200	Active TSS	NHLF	lung
7	chr2:114512000-114515400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:114512200-114514800	Active TSS	NHEK	skin
9	chr2:114512200-114515000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:114512200-114515000	Active TSS	GM12878-XiMat	blood
11	chr2:114512200-114515200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:114512200-114515200	Active TSS	HSMM	muscle
13	chr2:114512200-114515400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:114512400-114514600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr2:114512400-114514600	Active TSS	Stomach Smooth Muscle	stomach
16	chr2:114512400-114514800	Active TSS	Fetal Kidney	kidney
17	chr2:114512400-114514800	Active TSS	Osteobl	bone
18	chr2:114512400-114515200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:114512400-114515200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:114512400-114515200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:114512400-114515200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:114512400-114515200	Active TSS	Fetal Intestine Large	intestine
23	chr2:114512400-114515200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:114512400-114515200	Active TSS	NH-A	brain
25	chr2:114512400-114515400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:114512400-114515400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:114512400-114515400	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr2:114512400-114515400	Active TSS	A549	lung
29	chr2:114512600-114514800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr2:114512600-114514800	Bivalent/Poised TSS	HepG2	liver
31	chr2:114512600-114515000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:114512600-114515000	Active TSS	Left Ventricle	heart
33	chr2:114512600-114515000	Active TSS	Ovary	ovary
34	chr2:114512600-114515200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:114512600-114515200	Active TSS	Aorta	Aorta
36	chr2:114512600-114515200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:114512600-114515200	Active TSS	Brain Substantia Nigra	brain
38	chr2:114512600-114515200	Active TSS	Esophagus	oesophagus
39	chr2:114512600-114515200	Active TSS	Fetal Intestine Small	intestine
40	chr2:114512600-114515200	Active TSS	Psoas Muscle	Psoas
41	chr2:114512600-114515200	Active TSS	Right Ventricle	heart
42	chr2:114512600-114515400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr2:114512600-114515400	Active TSS	Fetal Stomach	stomach
44	chr2:114512600-114515400	Active TSS	Hela-S3	cervix
45	chr2:114512800-114514800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:114512800-114514800	Active TSS	Fetal Lung	lung
47	chr2:114512800-114514800	Active TSS	Fetal Muscle Trunk	muscle
48	chr2:114512800-114514800	Active TSS	Fetal Muscle Leg	muscle
49	chr2:114512800-114515200	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr2:114512800-114515200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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