Variant report

Variant	rs1454421
Chromosome Location	chr2:55647322-55647323
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	MYC	chr2:55646122-55647864	K562	blood:	n/a	chr2:55647250-55647259
2	RCOR1	chr2:55645939-55647543	K562	blood:	n/a	n/a
3	BHLHE40	chr2:55646315-55648449	GM12878	blood:	n/a	chr2:55647260-55647276
4	TAF1	chr2:55646233-55647565	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr2:55646809-55647348	GM12878	blood:	n/a	chr2:55647118-55647130 chr2:55647119-55647133 chr2:55647323-55647332 chr2:55647120-55647129 chr2:55647019-55647030 chr2:55647020-55647030 chr2:55647322-55647334 chr2:55647119-55647128 chr2:55647119-55647128
6	BCL3	chr2:55646230-55647945	A549	lung:	n/a	chr2:55647787-55647796 chr2:55647092-55647101 chr2:55647231-55647244
7	POLR2A	chr2:55647199-55647517	HepG2	liver:	n/a	n/a
8	PBX3	chr2:55646678-55647436	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr2:55646629-55647370	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr2:55645815-55647620	GM12891	blood:	n/a	n/a
11	MAZ	chr2:55646343-55647550	GM12878	blood:	n/a	chr2:55647250-55647259
12	MEF2A	chr2:55646886-55647377	K562	blood:	n/a	n/a
13	MYC	chr2:55645887-55647919	NB4	blood:	n/a	chr2:55647250-55647259
14	SIN3AK20	chr2:55646558-55647404	HepG2	liver:	n/a	n/a
15	JUN	chr2:55646761-55647358	K562	blood:	n/a	n/a
16	JUN	chr2:55645058-55648415	K562	blood:	n/a	chr2:55647729-55647736 chr2:55647728-55647739 chr2:55645468-55645477 chr2:55647729-55647737 chr2:55647729-55647737
17	JUND	chr2:55646854-55647804	H1-hESC	embryonic stem cell:	n/a	chr2:55647729-55647736 chr2:55647728-55647739 chr2:55647729-55647737 chr2:55647729-55647737
18	POLR2A	chr2:55647204-55647455	GM12891	blood:	n/a	n/a
19	TAF7	chr2:55646332-55647378	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:55646600-55647605	K562	blood:	n/a	n/a
21	E2F4	chr2:55646867-55647765	MCF10A-Er-Src	breast:	n/a	chr2:55647254-55647268 chr2:55647193-55647202 chr2:55647251-55647265 chr2:55647235-55647244 chr2:55647231-55647240
22	SIN3A	chr2:55646119-55647828	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr2:55645746-55647971	HepG2	liver:	n/a	chr2:55647250-55647259
24	POLR2A	chr2:55646417-55647518	GM12892	blood:	n/a	n/a
25	RAD21	chr2:55646751-55647474	Hela-S3	cervix:	n/a	chr2:55647221-55647235
26	SRF	chr2:55646926-55647553	GM12878	blood:	n/a	chr2:55647120-55647130
27	EP300	chr2:55646228-55647701	A549	lung:	n/a	chr2:55647228-55647244 chr2:55647062-55647071 chr2:55647235-55647244 chr2:55647261-55647277
28	POLR2A	chr2:55646400-55647487	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr2:55646345-55647491	PANC-1	pancreas:	n/a	n/a
30	WRNIP1	chr2:55646950-55647830	GM12878	blood:	n/a	n/a
31	IKZF1	chr2:55645867-55647696	GM12878	blood:	n/a	n/a
32	GABPA	chr2:55646777-55647394	K562	blood:	n/a	chr2:55647235-55647244 chr2:55647323-55647332
33	HEY1	chr2:55646732-55647474	HepG2	liver:	n/a	n/a
34	SRF	chr2:55647194-55647494	GM12878	blood:	n/a	n/a
35	ZBTB7A	chr2:55646331-55647327	K562	blood:	n/a	n/a
36	YY1	chr2:55646563-55647676	SK-N-SH_RA	brain:	n/a	chr2:55647231-55647240 chr2:55647231-55647245 chr2:55647232-55647246 chr2:55647213-55647222
37	POLR2A	chr2:55646786-55647439	K562	blood:	n/a	n/a
38	EP300	chr2:55646980-55647366	K562	blood:	n/a	chr2:55647228-55647244 chr2:55647062-55647071 chr2:55647235-55647244 chr2:55647261-55647277
39	ZEB1	chr2:55646836-55647354	GM12878	blood:	n/a	n/a
40	TBP	chr2:55646853-55647534	GM12878	blood:	n/a	n/a
41	CTBP2	chr2:55646559-55647340	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr2:55646246-55647555	MCF10A-Er-Src	breast:	n/a	n/a
43	NRF1	chr2:55647087-55647549	GM12878	blood:	n/a	chr2:55647235-55647244 chr2:55647323-55647332
44	POLR2A	chr2:55646258-55647337	HUVEC	blood vessel:	n/a	n/a
45	TEAD4	chr2:55646686-55647417	HepG2	liver:	n/a	n/a
46	PML	chr2:55645861-55647868	GM12878	blood:	n/a	n/a
47	EP300	chr2:55646613-55647472	ECC-1	luminal epithelium:	n/a	chr2:55647228-55647244 chr2:55647062-55647071 chr2:55647235-55647244 chr2:55647261-55647277
48	HEY1	chr2:55646315-55647459	K562	blood:	n/a	n/a
49	ELK4	chr2:55647314-55647564	Hela-S3	cervix:	n/a	n/a
50	REST	chr2:55646259-55647358	HepG2	liver:	n/a	chr2:55647085-55647098

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55646515..55647331-chr6:7541599..7542577,2	Hela-S3	cervix:
3	chr1:110881811..110882732-chr2:55647017..55647547,2	Hela-S3	cervix:
4	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
5	chr1:150551620..150552286-chr2:55646665..55647534,2	Hela-S3	cervix:
6	chr2:55459243..55461012-chr2:55645151..55647509,2	MCF-7	breast:
7	chr2:55645285..55648583-chr2:55745099..55748276,4	K562	blood:
8	chr2:55507859..55511177-chr2:55645007..55647398,3	K562	blood:
9	chr2:55647253..55647758-chr2:55659096..55659834,2	K562	blood:
10	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:
11	chr1:89457947..89458558-chr2:55646643..55647391,2	Hela-S3	cervix:
12	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
13	chr2:55646864..55647857-chr2:70417660..70418658,2	Hela-S3	cervix:
14	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC104-5	chr2:55646412-55648361	NONHSAT070787

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000162997	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000162775	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000115998	Chromatin interaction
ENSG00000163001	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000213516	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000137944	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000096696	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10865285	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11125567	0.84[EUR][1000 genomes]
rs11680143	0.84[EUR][1000 genomes]
rs11692239	0.84[EUR][1000 genomes]
rs12470528	0.84[EUR][1000 genomes]
rs12471421	0.81[AMR][1000 genomes]
rs12476508	0.82[EUR][1000 genomes]
rs12476548	0.84[EUR][1000 genomes]
rs1545555	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1902059	0.84[EUR][1000 genomes]
rs1982484	0.81[EUR][1000 genomes]
rs2198577	0.82[AMR][1000 genomes]
rs2576713	0.82[EUR][1000 genomes]
rs2576714	0.82[EUR][1000 genomes]
rs2576715	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2589073	0.83[EUR][1000 genomes]
rs2589075	0.84[EUR][1000 genomes]
rs2589077	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2589102	0.81[AFR][1000 genomes]
rs2864830	0.80[AFR][1000 genomes]
rs2867180	0.84[EUR][1000 genomes]
rs2867181	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2903508	0.82[EUR][1000 genomes]
rs2917778	0.82[EUR][1000 genomes]
rs2920964	0.85[EUR][1000 genomes]
rs3099075	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099076	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099077	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099079	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099082	0.80[AFR][1000 genomes]
rs3099084	0.80[AFR][1000 genomes]
rs3111404	0.85[EUR][1000 genomes]
rs3111410	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3111411	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3111412	0.80[AFR][1000 genomes]
rs3111413	0.85[EUR][1000 genomes]
rs35963448	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3762510	0.82[EUR][1000 genomes]
rs3762512	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791653	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4349381	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4672039	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55711116	0.84[EUR][1000 genomes]
rs55828034	0.80[EUR][1000 genomes]
rs55908714	0.84[EUR][1000 genomes]
rs57410428	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61379198	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137154	0.84[EUR][1000 genomes]
rs62137157	0.84[EUR][1000 genomes]
rs6545493	0.80[AMR][1000 genomes]
rs6706178	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6718236	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6725124	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7425220	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7561210	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7564292	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7570934	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582580	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586529	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454421	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55642600-55648200	Active TSS	GM12878-XiMat	blood
2	chr2:55643000-55648000	Active TSS	Brain Germinal Matrix	brain
3	chr2:55643200-55647600	Active TSS	K562	blood
4	chr2:55643200-55648000	Active TSS	Fetal Brain Female	brain
5	chr2:55643200-55648200	Active TSS	Brain Cingulate Gyrus	brain
6	chr2:55643200-55648200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:55643600-55647600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:55643800-55648000	Active TSS	NHDF-Ad	bronchial
9	chr2:55643800-55648400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:55643800-55648400	Active TSS	NHLF	lung
11	chr2:55644000-55647400	Active TSS	HMEC	breast
12	chr2:55644000-55647600	Active TSS	Hela-S3	cervix
13	chr2:55644000-55648000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:55644000-55648000	Active TSS	Brain Angular Gyrus	brain
15	chr2:55644000-55648000	Active TSS	Brain Substantia Nigra	brain
16	chr2:55644000-55648400	Active TSS	Brain Anterior Caudate	brain
17	chr2:55644200-55647600	Active TSS	Primary monocytes fromperipheralblood	blood
18	chr2:55644200-55647600	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr2:55644200-55647800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:55644200-55647800	Active TSS	Brain Hippocampus Middle	brain
21	chr2:55644200-55648000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:55644200-55648200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr2:55644200-55648400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:55644400-55647600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:55644400-55647600	Active TSS	Fetal Muscle Leg	muscle
26	chr2:55644400-55647800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:55644400-55647800	Active TSS	Duodenum Mucosa	Duodenum
28	chr2:55644400-55647800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr2:55644400-55648000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:55644400-55648000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:55644400-55648000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:55644400-55648000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:55644400-55648000	Active TSS	Fetal Kidney	kidney
34	chr2:55644400-55648000	Active TSS	HSMMtube	muscle
35	chr2:55644400-55648200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr2:55644600-55647600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:55644600-55647600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:55644600-55647800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:55644600-55647800	Active TSS	HSMM	muscle
40	chr2:55644600-55647800	Active TSS	NH-A	brain
41	chr2:55644600-55648000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:55644600-55648000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:55644600-55648000	Active TSS	Fetal Stomach	stomach
44	chr2:55644600-55648200	Active TSS	A549	lung
45	chr2:55644800-55647400	Active TSS	NHEK	skin
46	chr2:55644800-55647600	Active TSS	Stomach Smooth Muscle	stomach
47	chr2:55644800-55647800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:55644800-55648000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:55644800-55648000	Active TSS	Osteobl	bone
50	chr2:55645000-55647800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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