Variant report

Variant	rs9462451
Chromosome Location	chr6:38671124-38671125
allele	A/G
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	MAX	chr6:38670416-38671273	A549	lung:	n/a	n/a
2	SP1	chr6:38670654-38671282	H1-hESC	embryonic stem cell:	n/a	chr6:38670958-38670979
3	POLR2A	chr6:38670304-38671154	GM12878	blood:	n/a	n/a
4	MAX	chr6:38670183-38671314	NB4	blood:	n/a	n/a
5	CREB1	chr6:38670690-38671165	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr6:38669892-38671278	K562	blood:	n/a	n/a
7	POLR2A	chr6:38669989-38671175	Raji	blood:	n/a	n/a
8	GTF2F1	chr6:38670242-38671239	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:38670510-38671223	SK-N-MC	brain:	n/a	n/a
10	STAT3	chr6:38670750-38671312	GM12878	blood:	n/a	n/a
11	FOSL2	chr6:38670639-38671309	SK-N-SH	brain:	n/a	chr6:38671009-38671019 chr6:38671009-38671019 chr6:38671130-38671142 chr6:38671008-38671020 chr6:38671010-38671018 chr6:38671006-38671017
12	POLR2A	chr6:38670274-38671209	MCF-7	breast:	n/a	n/a
13	IRF1	chr6:38670699-38671253	K562	blood:	n/a	chr6:38670959-38670968 chr6:38671228-38671241 chr6:38671227-38671241 chr6:38671228-38671241 chr6:38671230-38671240 chr6:38671236-38671248 chr6:38671230-38671241 chr6:38671226-38671240
14	RCOR1	chr6:38670463-38671143	HepG2	liver:	n/a	n/a
15	YY1	chr6:38670678-38671155	HCT-116	colon:	n/a	chr6:38670930-38670944
16	POLR2A	chr6:38670292-38671181	K562	blood:	n/a	n/a
17	CBX3	chr6:38669869-38671234	K562	blood:	n/a	n/a
18	SP1	chr6:38670667-38671299	HepG2	liver:	n/a	chr6:38670958-38670979
19	ZNF143	chr6:38670657-38671296	H1-hESC	embryonic stem cell:	n/a	chr6:38671112-38671130 chr6:38671049-38671058 chr6:38671047-38671056 chr6:38671047-38671065
20	POLR2A	chr6:38670053-38671131	GM18505	blood:	n/a	n/a
21	HEY1	chr6:38669904-38671138	K562	blood:	n/a	n/a
22	JUN	chr6:38670385-38671340	K562	blood:	n/a	chr6:38671009-38671019 chr6:38671009-38671019 chr6:38671130-38671142 chr6:38671008-38671020 chr6:38671010-38671018 chr6:38671006-38671017
23	POLR2A	chr6:38669802-38671176	GM12892	blood:	n/a	n/a
24	STAT1	chr6:38670615-38671232	GM12878	blood:	n/a	n/a
25	STAT3	chr6:38670889-38671141	MCF10A-Er-Src	breast:	n/a	n/a
26	ELK1	chr6:38670575-38671237	Hela-S3	cervix:	n/a	n/a
27	BHLHE40	chr6:38670363-38671140	K562	blood:	n/a	n/a
28	TBP	chr6:38670684-38671261	GM12878	blood:	n/a	n/a
29	JUN	chr6:38670574-38671309	K562	blood:	n/a	chr6:38671009-38671019 chr6:38671009-38671019 chr6:38671130-38671142 chr6:38671008-38671020 chr6:38671010-38671018 chr6:38671006-38671017
30	MAX	chr6:38669973-38671239	HepG2	liver:	n/a	n/a
31	FOXA2	chr6:38670778-38671334	HepG2	liver:	n/a	chr6:38671154-38671166
32	NFYA	chr6:38670809-38671133	GM12878	blood:	n/a	n/a
33	SIX5	chr6:38670585-38671385	A549	lung:	n/a	chr6:38671049-38671058 chr6:38670601-38670615 chr6:38671047-38671056
34	YY1	chr6:38670283-38671323	SK-N-SH	brain:	n/a	chr6:38670930-38670944
35	ATF3	chr6:38670790-38671260	K562	blood:	n/a	n/a
36	TBL1XR1	chr6:38670563-38671214	GM12878	blood:	n/a	n/a
37	RFX5	chr6:38670782-38671232	GM12878	blood:	n/a	n/a
38	HCFC1	chr6:38669987-38671562	Hela-S3	cervix:	n/a	n/a
39	KAP1	chr6:38670273-38671274	K562	blood:	n/a	chr6:38671128-38671136
40	EGR1	chr6:38670711-38671132	GM12878	blood:	n/a	chr6:38671046-38671070
41	SMC3	chr6:38670719-38671136	Hela-S3	cervix:	n/a	n/a
42	YY1	chr6:38670602-38671199	K562	blood:	n/a	chr6:38670930-38670944
43	FOXM1	chr6:38670632-38671250	GM12878	blood:	n/a	n/a
44	REST	chr6:38670326-38671334	H1-neurons	neurons:	n/a	chr6:38670968-38670981 chr6:38670709-38670722
45	CREB1	chr6:38670603-38671315	HepG2	liver:	n/a	n/a
46	EP300	chr6:38670853-38671177	GM12878	blood:	n/a	chr6:38671095-38671109 chr6:38671096-38671110 chr6:38671094-38671108
47	ARID3A	chr6:38670777-38671373	HepG2	liver:	n/a	n/a
48	ELF1	chr6:38670824-38671135	HepG2	liver:	n/a	n/a
49	GTF2F1	chr6:38670542-38671268	K562	blood:	n/a	n/a
50	YY1	chr6:38670400-38671173	A549	lung:	n/a	chr6:38670930-38670944

No.	Distal block	Cell Line	Cell type
1	chr6:38670885..38672648-chr6:38689794..38692471,2	K562	blood:
2	chr15:81292668..81293610-chr6:38670574..38671160,2	Hela-S3	cervix:
3	chr1:149223865..149224475-chr6:38670785..38671479,2	Hela-S3	cervix:
4	chr6:38606797..38609056-chr6:38670128..38671908,2	K562	blood:
5	chr6:38650801..38652839-chr6:38670478..38672074,2	MCF-7	breast:

Variant related genes	Relation type
GLO1	TF binding region
ENSG00000124767	Chromatin interaction
ENSG00000140406	Chromatin interaction
ENSG00000124721	Chromatin interaction
ENSG00000183826	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10947757	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1130534	0.97[ASN][1000 genomes]
rs1579028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1621483	0.92[ASN][1000 genomes]
rs3799703	0.92[JPT][hapmap]
rs4711553	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4711556	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714173	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4714174	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs57156564	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58749921	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59793635	0.84[ASN][1000 genomes]
rs60262339	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925790	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs6931745	0.84[ASN][1000 genomes]
rs6932648	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7767791	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7774234	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7775968	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9296255	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs9366969	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9369073	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9369075	0.97[ASN][1000 genomes]
rs937662	0.92[JPT][hapmap]
rs9380763	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9394516	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9394519	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9394522	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9394523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[ASN][1000 genomes]
rs9394524	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9462446	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9462448	0.92[JPT][hapmap]
rs9462453	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9470901	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9470902	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs9470913	0.84[ASN][1000 genomes]
rs9470916	0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs9470917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38669000-38671400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:38669200-38671400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:38669400-38671200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:38669400-38671200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:38669400-38671400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:38669400-38671400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:38669400-38671400	Active TSS	NHLF	lung
8	chr6:38669600-38671200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:38669600-38671200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:38669600-38671200	Active TSS	K562	blood
11	chr6:38669600-38671400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:38669600-38671400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:38669800-38671200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:38669800-38671200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:38669800-38671200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:38669800-38671200	Active TSS	Duodenum Mucosa	Duodenum
17	chr6:38669800-38671200	Active TSS	GM12878-XiMat	blood
18	chr6:38669800-38671400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:38669800-38671400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:38669800-38671400	Active TSS	Stomach Smooth Muscle	stomach
21	chr6:38669800-38671400	Active TSS	NH-A	brain
22	chr6:38669800-38671600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:38669800-38671600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:38670000-38671200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:38670000-38671200	Active TSS	NHDF-Ad	bronchial
26	chr6:38670000-38671400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:38670000-38671400	Active TSS	Placenta	Placenta
28	chr6:38670000-38671400	Active TSS	Right Atrium	heart
29	chr6:38670000-38671400	Active TSS	A549	lung
30	chr6:38670200-38671200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr6:38670200-38671200	Active TSS	Brain Anterior Caudate	brain
32	chr6:38670200-38671400	Active TSS	Brain Hippocampus Middle	brain
33	chr6:38670200-38671400	Active TSS	Colon Smooth Muscle	Colon
34	chr6:38670400-38671200	Active TSS	Brain Cingulate Gyrus	brain
35	chr6:38670400-38671200	Active TSS	Dnd41	blood
36	chr6:38670400-38671400	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr6:38670400-38671400	Active TSS	Brain Angular Gyrus	brain
38	chr6:38670400-38671400	Active TSS	Fetal Lung	lung
39	chr6:38670400-38671400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr6:38670400-38671600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:38670400-38671600	Active TSS	Osteobl	bone
42	chr6:38670600-38671200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr6:38670600-38671200	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr6:38670600-38671400	Active TSS	Adipose Nuclei	Adipose
45	chr6:38670600-38671400	Active TSS	Fetal Muscle Leg	muscle
46	chr6:38670600-38671400	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr6:38670800-38671200	Weak transcription	Fetal Heart	heart
48	chr6:38670800-38671200	Active TSS	Thymus	Thymus
49	chr6:38670800-38671200	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:38671000-38671200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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