Variant report

Variant	rs10468829
Chromosome Location	chr18:29238454-29238455
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	STAT3	chr18:29237521-29239353	GM12878	blood:	n/a	chr18:29239109-29239120 chr18:29239163-29239171
2	IRF4	chr18:29238084-29239370	GM12878	blood:	n/a	chr18:29239107-29239121
3	POU2F2	chr18:29238196-29239421	GM12891	blood:	n/a	chr18:29239307-29239321
4	PAX5	chr18:29238299-29238680	GM12891	blood:	n/a	n/a
5	POLR2A	chr18:29238064-29238562	GM12891	blood:	n/a	n/a
6	EGR1	chr18:29238283-29238655	GM12878	blood:	n/a	n/a
7	YY1	chr18:29238248-29238528	K562	blood:	n/a	n/a
8	PML	chr18:29237949-29239747	GM12878	blood:	n/a	n/a
9	POLR2A	chr18:29237958-29239807	GM12892	blood:	n/a	n/a
10	POLR2A	chr18:29237796-29239666	GM12878	blood:	n/a	n/a
11	POLR2A	chr18:29238141-29238526	GM12891	blood:	n/a	n/a
12	SP1	chr18:29238106-29239207	GM12878	blood:	n/a	n/a
13	NFATC1	chr18:29237972-29239453	GM12878	blood:	n/a	n/a
14	SP1	chr18:29238047-29239145	GM12878	blood:	n/a	n/a
15	POLR2A	chr18:29238036-29238742	GM12892	blood:	n/a	n/a
16	POLR2A	chr18:29238205-29238478	GM12878	blood:	n/a	n/a
17	PAX5	chr18:29238199-29238673	GM12878	blood:	n/a	n/a
18	KAP1	chr18:29237768-29239557	HEK293	kidney:	n/a	n/a
19	RELA	chr18:29237955-29239773	GM18505	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
20	ZNF384	chr18:29237966-29238965	GM12878	blood:	n/a	n/a
21	POLR2A	chr18:29237860-29239780	GM12878	blood:	n/a	n/a
22	IKZF1	chr18:29238036-29239829	GM12878	blood:	n/a	chr18:29239650-29239662
23	BHLHE40	chr18:29237674-29239466	GM12878	blood:	n/a	chr18:29238322-29238338
24	SETDB1	chr18:29238335-29239431	U2OS	brain:	n/a	n/a
25	MAZ	chr18:29238141-29239407	GM12878	blood:	n/a	n/a
26	CHD2	chr18:29237844-29239383	GM12878	blood:	n/a	n/a
27	USF2	chr18:29238246-29239167	GM12878	blood:	n/a	chr18:29238322-29238338
28	BCLAF1	chr18:29238107-29239504	GM12878	blood:	n/a	chr18:29239218-29239227 chr18:29239109-29239118
29	RCOR1	chr18:29237814-29239273	GM12878	blood:	n/a	n/a
30	CEBPB	chr18:29238027-29239840	GM12878	blood:	n/a	chr18:29239160-29239173
31	RUNX3	chr18:29237656-29239864	GM12878	blood:	n/a	n/a
32	STAT1	chr18:29238174-29238977	GM12878	blood:	n/a	n/a
33	EP300	chr18:29238204-29239447	GM12878	blood:	n/a	chr18:29238975-29238982
34	POU2F2	chr18:29238121-29239520	GM12878	blood:	n/a	chr18:29239307-29239321
35	PAX5	chr18:29238131-29238691	GM12878	blood:	n/a	n/a
36	RELA	chr18:29238158-29239806	GM10847	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
37	RELA	chr18:29237882-29239843	GM12891	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
38	POLR2A	chr18:29237866-29239572	GM19099	blood:	n/a	n/a
39	RELA	chr18:29237876-29239806	GM15510	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
40	RELA	chr18:29237812-29239830	GM19193	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
41	MXI1	chr18:29237701-29239709	GM12878	blood:	n/a	n/a
42	POU2F2	chr18:29238306-29238664	GM12878	blood:	n/a	n/a
43	YY1	chr18:29238078-29238797	GM12878	blood:	n/a	n/a
44	STAT5A	chr18:29238068-29239234	GM12878	blood:	n/a	chr18:29239109-29239120 chr18:29239163-29239171
45	CREB1	chr18:29238099-29239509	GM12878	blood:	n/a	n/a
46	EBF1	chr18:29238057-29239129	GM12878	blood:	n/a	chr18:29238238-29238249
47	POLR2A	chr18:29238006-29239635	GM12878	blood:	n/a	n/a
48	ELK1	chr18:29238190-29239057	GM12878	blood:	n/a	n/a
49	PAX5	chr18:29238015-29239152	GM12878	blood:	n/a	chr18:29239109-29239118
50	MEF2A	chr18:29238051-29239269	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29235239..29238459-chr18:29263541..29266170,4	MCF-7	breast:

Variant related genes	Relation type
B4GALT6	TF binding region
ENSG00000118276	Chromatin interaction
ENSG00000259985	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs16962266	1.00[CEU][hapmap]
rs17803358	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr18:29204600-29238600	Weak transcription	Gastric	stomach
3	chr18:29219200-29240000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr18:29227800-29238800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr18:29227800-29240800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:29229200-29245200	Weak transcription	Brain Anterior Caudate	brain
10	chr18:29229400-29238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:29229400-29239600	Weak transcription	Brain Hippocampus Middle	brain
12	chr18:29229400-29239600	Weak transcription	Right Atrium	heart
13	chr18:29229400-29252800	Weak transcription	NHEK	skin
14	chr18:29229600-29239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:29231200-29242400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:29231800-29251800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr18:29233000-29239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr18:29233200-29238800	Weak transcription	Fetal Thymus	thymus
19	chr18:29233400-29238600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr18:29234400-29238600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr18:29235600-29239000	Weak transcription	Fetal Brain Female	brain
22	chr18:29235600-29254800	Weak transcription	HUVEC	blood vessel
23	chr18:29235600-29257800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:29236400-29239200	Weak transcription	Small Intestine	intestine
25	chr18:29237000-29240000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr18:29237000-29240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr18:29237400-29239800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr18:29237400-29240000	Enhancers	Fetal Intestine Small	intestine
29	chr18:29237400-29243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:29237600-29239600	Strong transcription	Dnd41	blood
31	chr18:29237600-29240000	Flanking Active TSS	GM12878-XiMat	blood
32	chr18:29237800-29238600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:29237800-29238600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr18:29237800-29239400	Enhancers	Primary B cells from cord blood	blood
35	chr18:29237800-29239600	Enhancers	Placenta	Placenta
36	chr18:29237800-29239800	Enhancers	Primary B cells from peripheral blood	blood
37	chr18:29238000-29238600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr18:29238000-29238600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr18:29238000-29239800	Enhancers	Duodenum Mucosa	Duodenum
40	chr18:29238000-29240000	Enhancers	Fetal Intestine Large	intestine
41	chr18:29238000-29240600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr18:29238200-29238600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr18:29238200-29238800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:29238200-29238800	Genic enhancers	Primary hematopoietic stem cells	blood
45	chr18:29238200-29239000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr18:29238200-29239200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr18:29238200-29239200	Enhancers	Fetal Lung	lung
48	chr18:29238200-29239200	Enhancers	Osteobl	bone
49	chr18:29238200-29239400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr18:29238200-29239600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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