Variant report

Variant	rs35271356
Chromosome Location	chr18:29266001-29266002
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	CHD2	chr18:29265095-29266137	GM12878	blood:	n/a	chr18:29265480-29265490 chr18:29265352-29265362
2	TAF1	chr18:29265118-29266086	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr18:29263962-29266139	GM18951	blood:	n/a	n/a
4	POLR2A	chr18:29265727-29266089	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr18:29264957-29266094	HepG2	liver:	n/a	n/a
6	STAT5A	chr18:29265086-29266160	GM12878	blood:	n/a	chr18:29265473-29265485 chr18:29266116-29266127
7	MAX	chr18:29264066-29266173	GM12878	blood:	n/a	n/a
8	RCOR1	chr18:29265134-29266129	GM12878	blood:	n/a	n/a
9	MAX	chr18:29264553-29266091	HepG2	liver:	n/a	n/a
10	PML	chr18:29263917-29266204	GM12878	blood:	n/a	n/a
11	MTA3	chr18:29264967-29266697	GM12878	blood:	n/a	n/a
12	MXI1	chr18:29265832-29266135	GM12878	blood:	n/a	n/a
13	NRF1	chr18:29265880-29266064	GM12878	blood:	n/a	n/a
14	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
15	MAX	chr18:29265487-29266115	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr18:29264354-29266101	GM10847	blood:	n/a	n/a
17	POLR2A	chr18:29264493-29266183	H1-hESC	embryonic stem cell:	n/a	n/a
18	YY1	chr18:29265532-29266479	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr18:29265077-29266162	H1-neurons	neurons:	n/a	n/a
20	YY1	chr18:29265827-29266103	A549	lung:	n/a	n/a
21	POLR2A	chr18:29264160-29266130	GM12878	blood:	n/a	n/a
22	YY1	chr18:29265794-29266246	GM12892	blood:	n/a	n/a
23	POLR2A	chr18:29265025-29266222	H1-neurons	neurons:	n/a	n/a
24	CHD1	chr18:29265709-29266202	GM12878	blood:	n/a	n/a
25	MYC	chr18:29265769-29266017	H1-hESC	embryonic stem cell:	n/a	n/a
26	NFIC	chr18:29265531-29266270	GM12878	blood:	n/a	n/a
27	POLR2A	chr18:29265602-29266162	GM12892	blood:	n/a	n/a
28	SIN3A	chr18:29263824-29266100	H1-hESC	embryonic stem cell:	n/a	chr18:29265439-29265452 chr18:29265145-29265158
29	POLR2A	chr18:29264143-29266339	GM18505	blood:	n/a	n/a
30	JUND	chr18:29265978-29266134	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr18:29264911-29266346	H1-neurons	neurons:	n/a	n/a
32	MAX	chr18:29264051-29266252	A549	lung:	n/a	n/a
33	RELA	chr18:29265105-29266014	GM15510	blood:	n/a	n/a
34	HA-E2F1	chr18:29265086-29266228	MCF-7	breast:	n/a	chr18:29265433-29265443 chr18:29265408-29265419
35	FOXM1	chr18:29265539-29266139	GM12878	blood:	n/a	n/a
36	POLR2A	chr18:29264009-29266286	GM12892	blood:	n/a	n/a
37	CTCF	chr18:29265958-29266048	GM19239	blood:	n/a	n/a
38	CTCF	chr18:29264988-29266099	A549	lung:	n/a	chr18:29265145-29265158
39	USF2	chr18:29265725-29266056	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr18:29264697-29266279	GM12878	blood:	n/a	n/a
41	BCLAF1	chr18:29265012-29266201	GM12878	blood:	n/a	chr18:29265139-29265152 chr18:29265437-29265450 chr18:29265359-29265368 chr18:29265809-29265818 chr18:29265348-29265357 chr18:29266138-29266147
42	YY1	chr18:29265759-29266122	SK-N-SH_RA	brain:	n/a	n/a
43	POLR2A	chr18:29263761-29266391	GM19099	blood:	n/a	n/a
44	TAF1	chr18:29265025-29266101	H1-hESC	embryonic stem cell:	n/a	n/a
45	SETDB1	chr18:29265708-29266262	U2OS	brain:	n/a	n/a
46	POLR2A	chr18:29265771-29266029	A549	lung:	n/a	n/a
47	POLR2A	chr18:29263999-29266298	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr18:29264508-29266381	SK-N-SH	brain:	n/a	chr18:29265145-29265158
49	ATF2	chr18:29265483-29266189	GM12878	blood:	n/a	n/a
50	KAP1	chr18:29265822-29266228	U2OS	brain:	n/a	n/a

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

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
ENSG00000118276	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12957312	1.00[ASN][1000 genomes]
rs12964359	1.00[ASN][1000 genomes]
rs12967431	1.00[ASN][1000 genomes]
rs12967606	1.00[ASN][1000 genomes]
rs12967642	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630405	1.00[ASN][1000 genomes]
rs1680645	1.00[ASN][1000 genomes]
rs17661987	1.00[ASN][1000 genomes]
rs17718389	1.00[ASN][1000 genomes]
rs17718513	1.00[ASN][1000 genomes]
rs2230234	1.00[ASN][1000 genomes]
rs34844920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34959937	1.00[ASN][1000 genomes]
rs35129944	1.00[ASN][1000 genomes]
rs35217404	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35703749	1.00[ASN][1000 genomes]
rs501570	1.00[ASN][1000 genomes]
rs616082	1.00[ASN][1000 genomes]
rs6506937	1.00[EUR][1000 genomes]
rs66534107	1.00[ASN][1000 genomes]
rs668996	1.00[ASN][1000 genomes]
rs71361333	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71361335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71361336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71361337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71361338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71361339	1.00[EUR][1000 genomes]
rs71361340	1.00[EUR][1000 genomes]
rs71361341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71361344	1.00[ASN][1000 genomes]
rs71361345	1.00[ASN][1000 genomes]
rs73409433	1.00[ASN][1000 genomes]
rs8083292	1.00[ASN][1000 genomes]
rs8083894	1.00[ASN][1000 genomes]
rs8084382	1.00[ASN][1000 genomes]
rs8084675	1.00[ASN][1000 genomes]
rs9952659	1.00[ASN][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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29262000-29266200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:29262600-29266400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr18:29263000-29266400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr18:29263200-29266200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:29263200-29266200	Active TSS	Brain Angular Gyrus	brain
6	chr18:29263200-29266200	Active TSS	Brain Cingulate Gyrus	brain
7	chr18:29263200-29266400	Active TSS	Brain Anterior Caudate	brain
8	chr18:29263200-29266400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr18:29263400-29266200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29263400-29266200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:29263600-29266200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr18:29263600-29266200	Active TSS	Colon Smooth Muscle	Colon
13	chr18:29263600-29266600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr18:29264000-29266200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr18:29264000-29266200	Active TSS	Brain Substantia Nigra	brain
16	chr18:29264000-29266400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:29264000-29266400	Active TSS	Fetal Kidney	kidney
18	chr18:29264200-29266400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr18:29264400-29266200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr18:29264400-29266200	Active TSS	Fetal Muscle Trunk	muscle
21	chr18:29264400-29266200	Active TSS	Hela-S3	cervix
22	chr18:29264600-29266200	Active TSS	Esophagus	oesophagus
23	chr18:29264600-29266200	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr18:29265400-29266400	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr18:29265600-29266200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr18:29265600-29266200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
27	chr18:29265600-29266200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
28	chr18:29265600-29266200	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr18:29265600-29266200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr18:29265600-29266200	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
31	chr18:29265600-29266200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr18:29265600-29266200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:29265600-29266200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr18:29265600-29266200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr18:29265600-29266200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr18:29265600-29266200	Active TSS	Fetal Brain Male	brain
37	chr18:29265600-29266200	Flanking Active TSS	Pancreas	Pancrea
38	chr18:29265600-29266200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr18:29265600-29266200	Flanking Active TSS	Right Ventricle	heart
40	chr18:29265600-29266200	Flanking Active TSS	HUVEC	blood vessel
41	chr18:29265600-29266200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr18:29265600-29266400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr18:29265600-29266400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr18:29265600-29266400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr18:29265600-29266400	Flanking Active TSS	Dnd41	blood
46	chr18:29265600-29266600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr18:29265600-29267600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr18:29265600-29267600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:29265600-29268000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:29265800-29266200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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