Variant report

Variant	rs12326244
Chromosome Location	chr18:29522302-29522303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:159)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:159 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:29522074-29524311	GM12878	blood:	n/a	n/a
2	YY1	chr18:29522266-29523222	K562	blood:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
3	EGR1	chr18:29522251-29522601	K562	blood:	n/a	chr18:29522413-29522427
4	POLR2A	chr18:29522016-29523663	MCF10A-Er-Src	breast:	n/a	n/a
5	ELF1	chr18:29522250-29522826	K562	blood:	n/a	chr18:29522343-29522356
6	POLR2A	chr18:29522017-29524380	HepG2	liver:	n/a	n/a
7	RCOR1	chr18:29522189-29523842	K562	blood:	n/a	n/a
8	EGR1	chr18:29522177-29522635	K562	blood:	n/a	chr18:29522413-29522427
9	POLR2A	chr18:29521981-29523799	PBDE	blood:	n/a	n/a
10	POLR2A	chr18:29522072-29523888	GM12891	blood:	n/a	n/a
11	CHD1	chr18:29522247-29523787	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:29522172-29523820	GM15510	blood:	n/a	n/a
13	SIN3A	chr18:29522284-29523836	GM12878	blood:	n/a	chr18:29523115-29523124
14	TBP	chr18:29522259-29523867	K562	blood:	n/a	n/a
15	MXI1	chr18:29522044-29523995	HepG2	liver:	n/a	n/a
16	POLR2A	chr18:29522128-29523810	MCF-7	breast:	n/a	n/a
17	POLR2A	chr18:29522266-29523241	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr18:29522191-29523244	K562	blood:	n/a	n/a
19	MYC	chr18:29522286-29524727	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
20	POLR2A	chr18:29522013-29523843	GM12892	blood:	n/a	n/a
21	POLR2A	chr18:29522156-29523894	H1-neurons	neurons:	n/a	n/a
22	BHLHE40	chr18:29522137-29523985	HepG2	liver:	n/a	chr18:29523112-29523125 chr18:29523114-29523123 chr18:29523115-29523124 chr18:29523108-29523129 chr18:29523114-29523123 chr18:29522742-29522758
23	STAT5A	chr18:29522070-29522734	GM12878	blood:	n/a	chr18:29522490-29522502
24	POLR2A	chr18:29522127-29523843	K562	blood:	n/a	n/a
25	BRCA1	chr18:29522228-29522501	Hela-S3	cervix:	n/a	n/a
26	SPI1	chr18:29522141-29522550	GM12891	blood:	n/a	chr18:29522480-29522493
27	POLR2A	chr18:29522219-29522614	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr18:29522197-29523228	K562	blood:	n/a	n/a
29	POLR2A	chr18:29522189-29523747	HUVEC	blood vessel:	n/a	n/a
30	STAT5A	chr18:29522176-29522633	GM12878	blood:	n/a	chr18:29522490-29522502
31	MAX	chr18:29522181-29524200	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
32	RELA	chr18:29522151-29524136	GM18505	blood:	n/a	n/a
33	POLR2A	chr18:29522157-29523556	HUVEC	blood vessel:	n/a	n/a
34	MXI1	chr18:29522235-29524175	Hela-S3	cervix:	n/a	n/a
35	ZMIZ1	chr18:29521994-29523655	K562	blood:	n/a	n/a
36	SIN3AK20	chr18:29522262-29522859	H1-hESC	embryonic stem cell:	n/a	n/a
37	REST	chr18:29522017-29524007	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr18:29522141-29523823	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr18:29522180-29523945	HL-60	blood:	n/a	n/a
40	MYC	chr18:29522168-29522520	K562	blood:	n/a	n/a
41	GATA1	chr18:29522205-29523184	PBDE	blood:	n/a	n/a
42	POLR2A	chr18:29522063-29523753	IMR90	lung:	n/a	n/a
43	POLR2A	chr18:29521877-29523673	K562	blood:	n/a	n/a
44	MXI1	chr18:29521941-29523997	IMR90	lung:	n/a	n/a
45	IRF1	chr18:29522209-29523801	K562	blood:	n/a	chr18:29523169-29523178 chr18:29523170-29523180 chr18:29523150-29523159 chr18:29523233-29523247 chr18:29522488-29522497 chr18:29523238-29523252
46	SPI1	chr18:29522020-29522729	HL-60	blood:	n/a	chr18:29522480-29522493
47	POLR2A	chr18:29522263-29523803	GM12892	blood:	n/a	n/a
48	PML	chr18:29522003-29523964	GM12878	blood:	n/a	n/a
49	RELA	chr18:29522157-29523862	GM12891	blood:	n/a	n/a
50	POLR2A	chr18:29522152-29523709	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:29522262-29522312	HRE	kidney:	n/a
2	chr18:29522262-29522312	GM19239	blood:	n/a
3	chr18:29522262-29522312	SKMC	muscle:	n/a
4	chr18:29522262-29522312	SAEC	small airway:	n/a
5	chr18:29522262-29522312	GM12892	blood:	n/a
6	chr18:29522262-29522312	Hela-S3	cervix:	n/a
7	chr18:29522262-29522312	AG09319	gingival:	n/a
8	chr18:29522262-29522312	CMK	blood:	n/a
9	chr18:29522262-29522312	NHDF-neo	bronchial:	n/a
10	chr18:29522262-29522312	AoSMC	blood vessel:	n/a
11	chr18:29522262-29522312	ovcar-3	ovarian:	n/a
12	chr18:29522262-29522312	HEK293	kidney:	embryo
13	chr18:29522262-29522312	NHBE	bronchial:	n/a
14	chr18:29522262-29522312	HepG2	liver:	n/a
15	chr18:29522262-29522312	HUVEC	blood vessel:	n/a
16	chr18:29522262-29522312	HCT-116	colon:	n/a
17	chr18:29522262-29522312	ECC-1	luminal epithelium:	n/a
18	chr18:29522262-29522312	NB4	blood:	n/a
19	chr18:29522262-29522312	Caco-2	colon:	n/a
20	chr18:29522262-29522312	AG04450	lung:	fetal
21	chr18:29522262-29522312	K562	blood:	n/a
22	chr18:29522262-29522312	RPTEC	kidney:	n/a
23	chr18:29522262-29522312	BJ	skin:	n/a
24	chr18:29522262-29522312	H1-hESC	embryonic stem cell:	embryo
25	chr18:29522262-29522312	HRCEpiC	kidney:	n/a
26	chr18:29522262-29522312	HCM	heart:	n/a
27	chr18:29522262-29522312	HPAEpiC	pulmonary alveolar:	n/a
28	chr18:29522262-29522312	HCF	heart:	n/a
29	chr18:29522262-29522312	HEEpiC	esophagus:	n/a
30	chr18:29522262-29522312	AG04449	skin:	fetal
31	chr18:29522262-29522312	HRPEpiC	eye:	n/a
32	chr18:29522262-29522312	PFSK-1	brain:	n/a
33	chr18:29522262-29522312	BE2_C	brain:	n/a
34	chr18:29522262-29522312	GM12878	blood:	n/a
35	chr18:29522262-29522312	AG10803	skin:	n/a
36	chr18:29522262-29522312	IMR90	lung:	fetal
37	chr18:29522262-29522312	ProgFib	skin:	n/a
38	chr18:29522262-29522312	HMEC	breast:	n/a
39	chr18:29522262-29522312	T-47D	breast:	n/a
40	chr18:29522262-29522312	NH-A	brain:	n/a
41	chr18:29522262-29522312	HIPEpiC	eye:	n/a
42	chr18:29522262-29522312	U87	brain:	n/a
43	chr18:29522262-29522312	HCPEpiC	choroid plexus:	n/a
44	chr18:29522262-29522312	GM12891	blood:	n/a
45	chr18:29522262-29522312	SK-N-SH	brain:	n/a
46	chr18:29522262-29522312	A549	lung:	n/a
47	chr18:29522262-29522312	HNPCEpiC	eye:	n/a
48	chr18:29522262-29522312	PrEC	prostate:	n/a
49	chr18:29522262-29522312	SK-N-SH_RA	brain:	n/a
50	chr18:29522262-29522312	MCF10A-Er-Src	breast:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:29517111..29520943-chr18:29521139..29523956,5	MCF-7	breast:
2	chr18:29522249..29524505-chr18:29596603..29599089,2	MCF-7	breast:
3	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
4	chr17:48942638..48944565-chr18:29522050..29524653,2	MCF-7	breast:
5	chr18:29518719..29521005-chr18:29521192..29525426,5	MCF-7	breast:
6	chr18:29450429..29452203-chr18:29521687..29523259,2	MCF-7	breast:
7	chr18:29521665..29524441-chr18:29544834..29547590,2	K562	blood:
8	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
9	chr18:29521522..29523729-chr18:29672844..29674625,2	MCF-7	breast:
10	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
11	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
12	chr18:29520544..29523172-chr18:33708356..33710539,2	K562	blood:

No data

Variant related genes	Relation type
TRAPPC8	TF binding region
ENSG00000263823	TF binding region
ENSG00000263823	CpG island
TRAPPC8	CpG island
ENSG00000134758	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000238982	Chromatin interaction
ENSG00000134759	Chromatin interaction
ENSG00000222320	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000141424	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000266105	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10153421	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12326219	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12327141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12709653	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12956638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12957365	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12957830	0.84[EUR][1000 genomes]
rs12959996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12963424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12963629	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12965515	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12965893	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12967531	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12968487	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2035418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291238	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28540496	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34011014	0.94[ASN][1000 genomes]
rs34846731	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36062390	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4581778	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7233820	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7244508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73954904	0.94[ASN][1000 genomes]
rs73958215	0.94[ASN][1000 genomes]
rs8084584	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8086196	0.94[ASN][1000 genomes]
rs8087104	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9675795	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9807439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29520200-29526800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:29521000-29522600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr18:29521000-29524400	Active TSS	Psoas Muscle	Psoas
4	chr18:29521200-29522600	Active TSS	Brain Germinal Matrix	brain
5	chr18:29521200-29524200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:29521200-29524400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:29521200-29524400	Active TSS	GM12878-XiMat	blood
8	chr18:29521200-29524800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr18:29521200-29524800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr18:29521200-29525200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr18:29521400-29522400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:29521400-29522400	Flanking Active TSS	Dnd41	blood
13	chr18:29521400-29522800	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr18:29521400-29523600	Active TSS	Muscle Satellite Cultured Cells	--
15	chr18:29521400-29524000	Active TSS	Ovary	ovary
16	chr18:29521400-29524000	Active TSS	NHDF-Ad	bronchial
17	chr18:29521400-29524000	Active TSS	NHLF	lung
18	chr18:29521400-29524200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:29521400-29524200	Active TSS	HSMM	muscle
20	chr18:29521400-29524400	Active TSS	Fetal Kidney	kidney
21	chr18:29521400-29524600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:29521400-29524600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr18:29521400-29525000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr18:29521400-29525400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr18:29521600-29522400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr18:29521600-29522400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr18:29521600-29522400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr18:29521600-29522400	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr18:29521600-29522400	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr18:29521600-29522400	Flanking Active TSS	Fetal Lung	lung
31	chr18:29521600-29522400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr18:29521600-29522400	Active TSS	Right Atrium	heart
33	chr18:29521600-29522400	Flanking Active TSS	HUVEC	blood vessel
34	chr18:29521600-29522400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr18:29521600-29522600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr18:29521600-29522600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr18:29521600-29523400	Active TSS	Colonic Mucosa	Colon
38	chr18:29521600-29523600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr18:29521600-29523800	Active TSS	Thymus	Thymus
40	chr18:29521600-29524000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:29521600-29524000	Active TSS	Aorta	Aorta
42	chr18:29521600-29524000	Active TSS	Fetal Intestine Small	intestine
43	chr18:29521600-29524200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:29521600-29524200	Active TSS	Fetal Intestine Large	intestine
45	chr18:29521600-29524200	Active TSS	Right Ventricle	heart
46	chr18:29521600-29524200	Active TSS	A549	lung
47	chr18:29521600-29524800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr18:29521600-29524800	Active TSS	HSMMtube	muscle
49	chr18:29521600-29525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr18:29521800-29522400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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