Variant report

Variant	rs2595371
Chromosome Location	chr18:29239188-29239189
allele	G/T
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	PML	chr18:29237949-29239747	GM12878	blood:	n/a	n/a
5	POLR2A	chr18:29237958-29239807	GM12892	blood:	n/a	n/a
6	POLR2A	chr18:29237796-29239666	GM12878	blood:	n/a	n/a
7	SP1	chr18:29238106-29239207	GM12878	blood:	n/a	n/a
8	NFATC1	chr18:29237972-29239453	GM12878	blood:	n/a	n/a
9	KAP1	chr18:29237768-29239557	HEK293	kidney:	n/a	n/a
10	RELA	chr18:29237955-29239773	GM18505	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
11	POLR2A	chr18:29237860-29239780	GM12878	blood:	n/a	n/a
12	IKZF1	chr18:29238036-29239829	GM12878	blood:	n/a	chr18:29239650-29239662
13	BHLHE40	chr18:29237674-29239466	GM12878	blood:	n/a	chr18:29238322-29238338
14	SETDB1	chr18:29238335-29239431	U2OS	brain:	n/a	n/a
15	MAZ	chr18:29238141-29239407	GM12878	blood:	n/a	n/a
16	CHD2	chr18:29237844-29239383	GM12878	blood:	n/a	n/a
17	BCLAF1	chr18:29238107-29239504	GM12878	blood:	n/a	chr18:29239218-29239227 chr18:29239109-29239118
18	RCOR1	chr18:29237814-29239273	GM12878	blood:	n/a	n/a
19	CEBPB	chr18:29238027-29239840	GM12878	blood:	n/a	chr18:29239160-29239173
20	RUNX3	chr18:29237656-29239864	GM12878	blood:	n/a	n/a
21	EP300	chr18:29238204-29239447	GM12878	blood:	n/a	chr18:29238975-29238982
22	POU2F2	chr18:29238121-29239520	GM12878	blood:	n/a	chr18:29239307-29239321
23	RELA	chr18:29238158-29239806	GM10847	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
24	RELA	chr18:29237882-29239843	GM12891	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
25	POLR2A	chr18:29237866-29239572	GM19099	blood:	n/a	n/a
26	PML	chr18:29238865-29239202	GM12878	blood:	n/a	n/a
27	RELA	chr18:29237876-29239806	GM15510	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
28	RELA	chr18:29237812-29239830	GM19193	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
29	MXI1	chr18:29237701-29239709	GM12878	blood:	n/a	n/a
30	STAT5A	chr18:29238068-29239234	GM12878	blood:	n/a	chr18:29239109-29239120 chr18:29239163-29239171
31	CREB1	chr18:29238099-29239509	GM12878	blood:	n/a	n/a
32	POLR2A	chr18:29238006-29239635	GM12878	blood:	n/a	n/a
33	MEF2A	chr18:29238051-29239269	GM12878	blood:	n/a	n/a
34	ATF2	chr18:29237694-29239617	GM12878	blood:	n/a	n/a
35	NFIC	chr18:29237949-29239681	GM12878	blood:	n/a	n/a
36	EP300	chr18:29237742-29239522	GM12878	blood:	n/a	chr18:29238975-29238982
37	POLR2A	chr18:29237765-29239658	GM12892	blood:	n/a	n/a
38	MTA3	chr18:29237969-29239915	GM12878	blood:	n/a	n/a
39	POLR2A	chr18:29237839-29239973	GM12891	blood:	n/a	n/a
40	BATF	chr18:29238824-29239246	GM12878	blood:	n/a	n/a
41	SPI1	chr18:29238866-29239305	GM12891	blood:	n/a	n/a
42	POLR2A	chr18:29238653-29239429	GM12891	blood:	n/a	n/a
43	POLR2A	chr18:29238771-29239531	GM12892	blood:	n/a	n/a
44	RELA	chr18:29237959-29239759	GM19099	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
45	CREB1	chr18:29238093-29239423	GM12878	blood:	n/a	n/a
46	BATF	chr18:29238187-29239273	GM12878	blood:	n/a	n/a
47	MAX	chr18:29238174-29239643	GM12878	blood:	n/a	n/a
48	IRF4	chr18:29238094-29239534	GM12878	blood:	n/a	chr18:29239107-29239121
49	RELA	chr18:29238143-29239773	GM18951	blood:	n/a	chr18:29239655-29239664 chr18:29239655-29239664
50	EP300	chr18:29237752-29239341	GM12878	blood:	n/a	chr18:29238975-29238982

Variant related genes	Relation type
B4GALT6	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11664340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1667273	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595370	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2848683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55817554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233900	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs7240561	0.86[GIH][hapmap]
rs9949056	1.00[CHB][hapmap]

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:63 , 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	chr18:29219200-29240000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr18:29227800-29240800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:29229200-29245200	Weak transcription	Brain Anterior Caudate	brain
8	chr18:29229400-29239600	Weak transcription	Brain Hippocampus Middle	brain
9	chr18:29229400-29239600	Weak transcription	Right Atrium	heart
10	chr18:29229400-29252800	Weak transcription	NHEK	skin
11	chr18:29229600-29239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr18:29231200-29242400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr18:29231800-29251800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr18:29233000-29239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:29235600-29254800	Weak transcription	HUVEC	blood vessel
16	chr18:29235600-29257800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:29236400-29239200	Weak transcription	Small Intestine	intestine
18	chr18:29237000-29240000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:29237000-29240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr18:29237400-29239800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr18:29237400-29240000	Enhancers	Fetal Intestine Small	intestine
22	chr18:29237400-29243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:29237600-29239600	Strong transcription	Dnd41	blood
24	chr18:29237600-29240000	Flanking Active TSS	GM12878-XiMat	blood
25	chr18:29237800-29239400	Enhancers	Primary B cells from cord blood	blood
26	chr18:29237800-29239600	Enhancers	Placenta	Placenta
27	chr18:29237800-29239800	Enhancers	Primary B cells from peripheral blood	blood
28	chr18:29238000-29239800	Enhancers	Duodenum Mucosa	Duodenum
29	chr18:29238000-29240000	Enhancers	Fetal Intestine Large	intestine
30	chr18:29238000-29240600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr18:29238200-29239200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr18:29238200-29239200	Enhancers	Fetal Lung	lung
33	chr18:29238200-29239200	Enhancers	Osteobl	bone
34	chr18:29238200-29239400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr18:29238200-29239600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:29238200-29239600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr18:29238200-29239600	Enhancers	Fetal Muscle Leg	muscle
38	chr18:29238200-29239800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr18:29238200-29239800	Enhancers	Psoas Muscle	Psoas
40	chr18:29238200-29239800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr18:29238400-29247000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr18:29238600-29239200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
43	chr18:29238600-29239200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr18:29238600-29239600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr18:29238600-29239600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:29238600-29239600	Enhancers	Adipose Nuclei	Adipose
47	chr18:29238600-29239600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr18:29238600-29240000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:29238600-29240200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr18:29238800-29239200	Enhancers	H9 Cell Line	embryonic stem cell

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