Variant report

Variant	rs968406
Chromosome Location	chr5:177035058-177035059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177034437-177035415	MCF10A-Er-Src	breast:	n/a	n/a
2	BRCA1	chr5:177034480-177035233	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP2	chr5:177034888-177035163	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr5:177034260-177035064	A549	lung:	n/a	n/a
5	ZNF143	chr5:177034405-177035250	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:177034206-177035152	H1-hESC	embryonic stem cell:	n/a	n/a
7	SMC3	chr5:177033978-177035334	SK-N-SH	brain:	n/a	n/a
8	JUND	chr5:177034390-177035323	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:177034441-177035452	K562	blood:	n/a	n/a
10	POLR2A	chr5:177034358-177035136	PANC-1	pancreas:	n/a	n/a
11	NFYB	chr5:177034785-177035085	Hela-S3	cervix:	n/a	chr5:177034984-177034999
12	CTCF	chr5:177034980-177035130	GM12874	blood:	n/a	n/a
13	NFYB	chr5:177034541-177035170	K562	blood:	n/a	chr5:177034984-177034999
14	POLR2A	chr5:177034087-177039636	SK-N-MC	brain:	n/a	n/a
15	MAX	chr5:177033933-177035134	MCF-7	breast:	n/a	n/a
16	POLR2A	chr5:177034477-177035206	H1-neurons	neurons:	n/a	n/a
17	SP1	chr5:177034646-177035121	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr5:177034384-177035221	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:177034240-177035372	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:177035050-177035239	HepG2	liver:	n/a	n/a
21	POLR2A	chr5:177034128-177035327	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr5:177034258-177035161	SK-N-SH	brain:	n/a	n/a
23	MYC	chr5:177034373-177035159	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr5:177034125-177035067	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:177035012-177035310	HUVEC	blood vessel:	n/a	n/a
26	CHD2	chr5:177034350-177035173	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr5:177034010-177035285	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:177034446-177035112	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:177034859-177035109	H1-hESC	embryonic stem cell:	n/a	n/a
30	BACH1	chr5:177034477-177035247	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr5:177033316-177035163	HepG2	liver:	n/a	n/a
32	SP1	chr5:177034369-177035215	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr5:177034785-177035294	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:177033922-177035244	GM12878	blood:	n/a	n/a
35	NFYB	chr5:177034779-177035176	GM12878	blood:	n/a	chr5:177034984-177034999
36	GTF2F1	chr5:177034277-177035107	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177032232..177035500-chr5:177036959..177040383,4	MCF-7	breast:
2	chr5:176956411..176959314-chr5:177032999..177035750,2	K562	blood:
3	chr5:176942970..176944777-chr5:177033617..177035543,2	MCF-7	breast:
4	chr5:176829222..176832099-chr5:177033371..177036238,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000247679	TF binding region
ENSG00000247679	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000146067	Chromatin interaction
ENSG00000131187	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10045871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10078930	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10479521	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11545868	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11960689	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12651744	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12656594	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28534743	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28738071	0.89[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs335487	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34705130	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976703	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6876792	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747861	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710333	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717102	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7720519	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7729422	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7731640	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9329062	0.90[AMR][1000 genomes];0.91[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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028000-177040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:177028200-177035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr5:177028200-177036400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
5	chr5:177028400-177036600	Weak transcription	HMEC	breast
6	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
8	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
10	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
11	chr5:177028400-177048400	Weak transcription	NH-A	brain
12	chr5:177028600-177041200	Weak transcription	Fetal Lung	lung
13	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
15	chr5:177028600-177053200	Weak transcription	HSMM	muscle
16	chr5:177028800-177044600	Weak transcription	GM12878-XiMat	blood
17	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
18	chr5:177029200-177045600	Weak transcription	Brain Angular Gyrus	brain
19	chr5:177030400-177039400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:177032000-177038800	Strong transcription	Dnd41	blood
21	chr5:177032800-177036400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:177032800-177045600	Weak transcription	HSMMtube	muscle
23	chr5:177033000-177045600	Weak transcription	Aorta	Aorta
24	chr5:177033200-177038600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:177033400-177035200	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr5:177033600-177035400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:177033600-177035400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:177033600-177035800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:177033600-177035800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr5:177033600-177035800	Weak transcription	Primary T cells from cord blood	blood
31	chr5:177033800-177035600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:177034000-177035200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:177034000-177035200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:177034000-177035200	Genic enhancers	Fetal Stomach	stomach
35	chr5:177034000-177035400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:177034000-177035400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:177034000-177035800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:177034000-177037200	Genic enhancers	Spleen	Spleen
39	chr5:177034200-177035200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:177034200-177035200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:177034200-177035200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr5:177034200-177035200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr5:177034200-177035200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr5:177034200-177035400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:177034200-177035600	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr5:177034200-177037000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:177034200-177040400	Strong transcription	Thymus	Thymus
48	chr5:177034400-177035200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr5:177034400-177035200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:177034400-177035200	Enhancers	Brain Cingulate Gyrus	brain

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