Variant report

Variant	rs73954671
Chromosome Location	chr18:29266219-29266220
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	GATA3	chr18:29266060-29266441	SH-SY5Y	brain:	n/a	chr18:29266061-29266068 chr18:29266138-29266148
2	MTA3	chr18:29264967-29266697	GM12878	blood:	n/a	n/a
3	YY1	chr18:29264744-29266279	GM12878	blood:	n/a	chr18:29265433-29265447 chr18:29265348-29265359 chr18:29265144-29265158 chr18:29265143-29265152 chr18:29264812-29264826 chr18:29264915-29264929 chr18:29264915-29264924 chr18:29264821-29264835
4	YY1	chr18:29265532-29266479	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr18:29265794-29266246	GM12892	blood:	n/a	n/a
6	POLR2A	chr18:29265025-29266222	H1-neurons	neurons:	n/a	n/a
7	NFIC	chr18:29265531-29266270	GM12878	blood:	n/a	n/a
8	POLR2A	chr18:29264143-29266339	GM18505	blood:	n/a	n/a
9	REST	chr18:29264911-29266346	H1-neurons	neurons:	n/a	n/a
10	MAX	chr18:29264051-29266252	A549	lung:	n/a	n/a
11	HA-E2F1	chr18:29265086-29266228	MCF-7	breast:	n/a	chr18:29265433-29265443 chr18:29265408-29265419
12	POLR2A	chr18:29264009-29266286	GM12892	blood:	n/a	n/a
13	POLR2A	chr18:29264697-29266279	GM12878	blood:	n/a	n/a
14	POLR2A	chr18:29263761-29266391	GM19099	blood:	n/a	n/a
15	SETDB1	chr18:29265708-29266262	U2OS	brain:	n/a	n/a
16	POLR2A	chr18:29263999-29266298	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr18:29264508-29266381	SK-N-SH	brain:	n/a	chr18:29265145-29265158
18	KAP1	chr18:29265822-29266228	U2OS	brain:	n/a	n/a
19	E2F6	chr18:29265101-29266221	H1-hESC	embryonic stem cell:	n/a	chr18:29265433-29265443 chr18:29265408-29265419
20	YY1	chr18:29264654-29266247	GM12878	blood:	n/a	chr18:29265433-29265447 chr18:29265348-29265359 chr18:29265144-29265158 chr18:29265143-29265152 chr18:29264812-29264826 chr18:29264915-29264929 chr18:29264915-29264924 chr18:29264821-29264835
21	EP300	chr18:29265110-29266232	GM12878	blood:	n/a	chr18:29265142-29265158 chr18:29265141-29265157
22	RELA	chr18:29265138-29266254	GM19099	blood:	n/a	n/a
23	YY1	chr18:29265512-29266337	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr18:29264111-29266224	GM19193	blood:	n/a	n/a
25	MTA3	chr18:29265545-29266290	GM12878	blood:	n/a	n/a
26	WRNIP1	chr18:29265716-29266437	GM12878	blood:	n/a	n/a
27	RELA	chr18:29265081-29266296	GM10847	blood:	n/a	n/a
28	POLR2A	chr18:29265571-29266313	GM12878	blood:	n/a	n/a
29	POLR2A	chr18:29263608-29266533	GM12878	blood:	n/a	n/a
30	GATA2	chr18:29265729-29266450	SH-SY5Y	brain:	n/a	chr18:29266061-29266068 chr18:29266138-29266148
31	POLR2A	chr18:29263972-29266236	GM12892	blood:	n/a	n/a
32	RELA	chr18:29263748-29266310	GM12891	blood:	n/a	n/a
33	POLR2A	chr18:29263652-29266352	GM12878	blood:	n/a	n/a
34	POLR2A	chr18:29264040-29266329	GM12878	blood:	n/a	n/a
35	POLR2A	chr18:29263995-29266247	GM12891	blood:	n/a	n/a
36	POLR2A	chr18:29263662-29267464	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29257336..29259422-chr18:29266158..29267928,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTR-1	chr18:29265618-29266786	ENSG00000259985.1
2	lnc-TTR-1	chr18:29264688-29267822	NONHSAT058829

Variant related genes	Relation type
B4GALT6	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs55705955	1.00[AFR][1000 genomes]
rs73954663	1.00[AMR][1000 genomes]
rs73954665	1.00[AMR][1000 genomes]
rs73954673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956430	1.00[AMR][1000 genomes]
rs73956433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8084949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3344706	chr18:29263704-29266352	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29262600-29266400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr18:29263000-29266400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr18:29263200-29266400	Active TSS	Brain Anterior Caudate	brain
4	chr18:29263200-29266400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr18:29263600-29266600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr18:29264000-29266400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr18:29264000-29266400	Active TSS	Fetal Kidney	kidney
8	chr18:29264200-29266400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr18:29265400-29266400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr18:29265600-29266400	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr18:29265600-29266400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr18:29265600-29266400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr18:29265600-29266400	Flanking Active TSS	Dnd41	blood
14	chr18:29265600-29266600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr18:29265600-29267600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr18:29265600-29267600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:29265600-29268000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:29265800-29266400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
19	chr18:29265800-29266400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr18:29265800-29266400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr18:29265800-29266400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr18:29265800-29266400	Flanking Active TSS	Fetal Thymus	thymus
23	chr18:29266000-29266400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:29266000-29266400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:29266000-29266400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr18:29266000-29266400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr18:29266000-29266400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr18:29266000-29266400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr18:29266000-29266400	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr18:29266000-29266400	Flanking Active TSS	A549	lung
31	chr18:29266000-29266800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr18:29266000-29267200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:29266000-29267200	Enhancers	HMEC	breast
34	chr18:29266000-29267400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:29266000-29267600	Flanking Active TSS	GM12878-XiMat	blood
36	chr18:29266200-29266400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr18:29266200-29266400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
38	chr18:29266200-29266400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr18:29266200-29266400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr18:29266200-29266400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr18:29266200-29266400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr18:29266200-29266400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr18:29266200-29266400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:29266200-29266400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:29266200-29266400	Enhancers	Adipose Nuclei	Adipose
46	chr18:29266200-29266400	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr18:29266200-29266400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr18:29266200-29266400	Active TSS	Fetal Brain Female	brain
49	chr18:29266200-29266400	Enhancers	Fetal Heart	heart
50	chr18:29266200-29266400	Enhancers	Fetal Lung	lung

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