Variant report

Variant	rs342550
Chromosome Location	chr5:16179125-16179126
allele	C/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	REST	chr5:16178912-16179172	GM12878	blood:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
2	MYC	chr5:16178963-16179220	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr5:16177252-16182613	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr5:16178933-16179535	H1-hESC	embryonic stem cell:	n/a	chr5:16179113-16179127
5	REST	chr5:16178898-16179339	SK-N-SH	brain:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
6	RCOR1	chr5:16178935-16179223	HepG2	liver:	n/a	n/a
7	SIN3AK20	chr5:16178940-16179151	PFSK-1	brain:	n/a	n/a
8	REST	chr5:16178580-16179556	H1-neurons	neurons:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
9	SIN3A	chr5:16178871-16179461	H1-hESC	embryonic stem cell:	n/a	chr5:16179072-16179086 chr5:16179071-16179081
10	YY1	chr5:16178893-16179284	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr5:16178932-16179194	PFSK-1	brain:	n/a	n/a
12	REST	chr5:16178850-16179327	GM12878	blood:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
13	REST	chr5:16178688-16179262	A549	lung:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
14	JUN	chr5:16178929-16179164	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr5:16178885-16179261	PANC-1	pancreas:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
16	RCOR1	chr5:16178957-16179235	K562	blood:	n/a	n/a
17	MYC	chr5:16179025-16179255	MCF-7	breast:	n/a	n/a
18	TBP	chr5:16178972-16179358	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr5:16178726-16179305	HepG2	liver:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
20	GATA3	chr5:16178936-16179278	T-47D	breast:	n/a	chr5:16178977-16178987
21	TCF12	chr5:16178948-16179248	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr5:16178828-16179450	SK-N-SH	brain:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
23	MAX	chr5:16178882-16179405	ECC-1	luminal epithelium:	n/a	n/a
24	REST	chr5:16178882-16179230	PANC-1	pancreas:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
25	REST	chr5:16178761-16179511	H1-hESC	embryonic stem cell:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
26	EGR1	chr5:16178924-16179279	H1-hESC	embryonic stem cell:	n/a	n/a
27	TEAD4	chr5:16178750-16179417	A549	lung:	n/a	n/a
28	REST	chr5:16178804-16179341	H1-hESC	embryonic stem cell:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
29	CTCF	chr5:16178992-16179431	MCF-7	breast:	n/a	chr5:16179111-16179124
30	REST	chr5:16178476-16179253	Hela-S3	cervix:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
31	REST	chr5:16178556-16179465	ECC-1	luminal epithelium:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
32	REST	chr5:16178858-16179280	HCT-116	colon:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
33	SIN3AK20	chr5:16178888-16179273	H1-hESC	embryonic stem cell:	n/a	n/a
34	REST	chr5:16178902-16179325	U87	brain:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
35	RAD21	chr5:16178931-16179493	H1-hESC	embryonic stem cell:	n/a	chr5:16179113-16179127
36	CTCF	chr5:16179047-16179173	MCF-7	breast:	n/a	chr5:16179111-16179124
37	REST	chr5:16178556-16179809	PFSK-1	brain:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
38	YY1	chr5:16178857-16179427	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZNF143	chr5:16178881-16179308	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr5:16178986-16179177	MCF-7	breast:	n/a	n/a
41	MAX	chr5:16178826-16179406	MCF-7	breast:	n/a	n/a
42	POLR2A	chr5:16179012-16179253	MCF-7	breast:	n/a	n/a
43	CBX3	chr5:16178898-16179206	K562	blood:	n/a	n/a
44	REST	chr5:16178879-16179254	PANC-1	pancreas:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
45	CTCF	chr5:16179010-16179444	MCF-7	breast:	n/a	chr5:16179111-16179124
46	CTCF	chr5:16179020-16179170	HBMEC	blood vessel:	n/a	chr5:16179111-16179124
47	REST	chr5:16178529-16179475	MCF-7	breast:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087
48	HMGN3	chr5:16179054-16179215	K562	blood:	n/a	n/a
49	SIN3AK20	chr5:16178959-16179248	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr5:16178510-16179799	ECC-1	luminal epithelium:	n/a	chr5:16179067-16179076 chr5:16179070-16179083 chr5:16179070-16179083 chr5:16179067-16179087 chr5:16179073-16179087 chr5:16179072-16179081 chr5:16179067-16179087 chr5:16179068-16179086 chr5:16179075-16179085 chr5:16179067-16179087

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16177598..16179739-chr5:16465554..16467569,2	MCF-7	breast:

Variant related genes	Relation type
MARCH11	TF binding region
ENSG00000250448	TF binding region
ENSG00000173545	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs168210	0.86[CEU][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs182922	0.81[CEU][hapmap];0.84[AFR][1000 genomes]
rs182942	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186899	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs237065	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342545	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs342548	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342556	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342557	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342559	1.00[CHB][hapmap]
rs344717	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830217	chr5:16004704-16225229	Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1838286	chr5:16150721-16180167	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1848638	chr5:16150721-16180167	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1793388	chr5:16159343-16179704	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv597297	chr5:16174133-16180115	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3407056	chr5:16177977-16180525	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3359354	chr5:16178477-16181525	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3498640	chr5:16178577-16181350	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3498642	chr5:16178577-16181350	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr5:16178000-16179400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:16178200-16179200	Active TSS	Brain Angular Gyrus	brain
3	chr5:16178200-16179400	Active TSS	Brain Anterior Caudate	brain
4	chr5:16178400-16179400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:16178400-16179400	Active TSS	Brain Cingulate Gyrus	brain
6	chr5:16178400-16179400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr5:16178600-16179400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
8	chr5:16178600-16179600	Enhancers	Gastric	stomach
9	chr5:16178600-16180200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:16178600-16181000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
11	chr5:16178800-16179200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:16178800-16179400	Bivalent/Poised TSS	NH-A	brain
13	chr5:16178800-16179800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:16178800-16180600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:16179000-16179200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:16179000-16179200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:16179000-16179200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:16179000-16179200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
19	chr5:16179000-16179200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr5:16179000-16179400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:16179000-16179400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr5:16179000-16179400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr5:16179000-16179400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:16179000-16179400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
25	chr5:16179000-16179400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
26	chr5:16179000-16179400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr5:16179000-16179400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:16179000-16179400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:16179000-16179400	Bivalent/Poised TSS	Colonic Mucosa	Colon
30	chr5:16179000-16179400	Bivalent Enhancer	Esophagus	oesophagus
31	chr5:16179000-16179400	Flanking Bivalent TSS/Enh	Left Ventricle	heart
32	chr5:16179000-16179400	Flanking Bivalent TSS/Enh	Ovary	ovary
33	chr5:16179000-16179400	Flanking Active TSS	Right Ventricle	heart
34	chr5:16179000-16179400	Bivalent Enhancer	Spleen	Spleen
35	chr5:16179000-16179400	Bivalent Enhancer	HMEC	breast
36	chr5:16179000-16179400	Active TSS	HSMM	muscle
37	chr5:16179000-16179400	Bivalent/Poised TSS	HSMMtube	muscle
38	chr5:16179000-16179600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:16179000-16179600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:16179000-16179600	Bivalent Enhancer	Psoas Muscle	Psoas
41	chr5:16179000-16179600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
42	chr5:16179000-16179800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr5:16179000-16179800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:16179000-16179800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:16179000-16180000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr5:16179000-16180000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:16179000-16180000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:16179000-16180000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:16179000-16180000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:16179000-16180000	Active TSS	Cortex derived primary cultured neurospheres	brain

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