Variant report

Variant	rs1146632
Chromosome Location	chr1:76251746-76251747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:435)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:435 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr1:76251494-76252412	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	HDAC2	chr1:76251533-76252016	HepG2	liver:	n/a	n/a
4	MAZ	chr1:76251261-76252176	K562	blood:	n/a	n/a
5	PML	chr1:76251098-76252684	K562	blood:	n/a	n/a
6	ZNF143	chr1:76251026-76252824	K562	blood:	n/a	n/a
7	MAFK	chr1:76251506-76252232	Hela-S3	cervix:	n/a	chr1:76252111-76252122
8	BCLAF1	chr1:76251314-76252604	K562	blood:	n/a	chr1:76252354-76252363
9	ZC3H11A	chr1:76251309-76252380	K562	blood:	n/a	n/a
10	ETS1	chr1:76251605-76252200	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:76251540-76252238	MCF-7	breast:	n/a	n/a
12	CHD2	chr1:76251674-76252067	HepG2	liver:	n/a	n/a
13	TCF3	chr1:76251729-76252135	GM12878	blood:	n/a	n/a
14	MYC	chr1:76250037-76254057	K562	blood:	n/a	chr1:76250221-76250231
15	ZNF384	chr1:76251491-76252497	K562	blood:	n/a	n/a
16	POLR2A	chr1:76251553-76252367	HepG2	liver:	n/a	n/a
17	FOS	chr1:76251564-76252140	MCF10A-Er-Src	breast:	n/a	n/a
18	REST	chr1:76251445-76252214	HepG2	liver:	n/a	chr1:76252048-76252062 chr1:76251977-76251986
19	ZBTB33	chr1:76251742-76252120	A549	lung:	n/a	n/a
20	ZKSCAN1	chr1:76251476-76252184	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr1:76251483-76252159	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:76250352-76252499	HCT-116	colon:	n/a	n/a
23	E2F4	chr1:76251602-76252217	MCF10A-Er-Src	breast:	n/a	n/a
24	TAF1	chr1:76251368-76252274	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr1:76251377-76252301	H1-hESC	embryonic stem cell:	n/a	n/a
26	FOXA2	chr1:76251666-76252114	HepG2	liver:	n/a	n/a
27	RCOR1	chr1:76251729-76252193	HepG2	liver:	n/a	n/a
28	SMC3	chr1:76251691-76251821	K562	blood:	n/a	n/a
29	POLR2A	chr1:76251285-76252190	GM12878	blood:	n/a	n/a
30	CHD2	chr1:76251655-76252555	GM12878	blood:	n/a	n/a
31	ELF1	chr1:76251690-76252214	MCF-7	breast:	n/a	n/a
32	CEBPB	chr1:76251343-76252182	K562	blood:	n/a	n/a
33	SIX5	chr1:76251656-76252093	GM12878	blood:	n/a	n/a
34	CBX3	chr1:76251341-76252267	K562	blood:	n/a	n/a
35	GATA2	chr1:76250970-76252516	SH-SY5Y	brain:	n/a	chr1:76251865-76251874 chr1:76252359-76252372
36	POU2F2	chr1:76251629-76252142	GM12878	blood:	n/a	n/a
37	TBP	chr1:76251350-76252806	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr1:76251251-76252235	GM12878	blood:	n/a	n/a
39	MBD4	chr1:76251553-76252269	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:76251046-76252580	GM12892	blood:	n/a	n/a
41	MYC	chr1:76251387-76252551	NB4	blood:	n/a	n/a
42	PML	chr1:76251509-76252299	GM12878	blood:	n/a	n/a
43	REST	chr1:76251447-76252240	K562	blood:	n/a	chr1:76252048-76252062 chr1:76251977-76251986
44	MBD4	chr1:76251538-76252157	HepG2	liver:	n/a	n/a
45	IRF1	chr1:76250035-76253994	K562	blood:	n/a	chr1:76250222-76250236
46	POLR2A	chr1:76251251-76252353	GM12878	blood:	n/a	n/a
47	MAX	chr1:76251618-76252395	A549	lung:	n/a	n/a
48	SIN3AK20	chr1:76251551-76252109	A549	lung:	n/a	n/a
49	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
50	MXI1	chr1:76251277-76252577	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76251676..76252625-chr15:72523942..72524487,2	Hela-S3	cervix:
2	chr1:76208509..76211228-chr1:76250454..76252141,2	K562	blood:
3	chr1:76189501..76190437-chr1:76251743..76252335,2	NB4	blood:
4	chr1:76251579..76252231-chr1:117664153..117664916,2	HCT-116	colon:
5	chr1:76189532..76190105-chr1:76251441..76252104,2	MCF-7	breast:
6	chr1:76190185..76192141-chr1:76251658..76253401,2	MCF-7	breast:
7	chr1:76251246..76251764-chr17:41437902..41438641,2	Hela-S3	cervix:
8	chr1:76251477..76252459-chr5:172571057..172571755,2	HCT-116	colon:
9	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
10	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
11	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
12	chr1:76251016..76253217-chr1:78469296..78471512,3	K562	blood:
13	chr1:76080033..76082466-chr1:76250224..76251859,2	MCF-7	breast:
14	chr1:76213297..76216875-chr1:76250212..76251937,3	K562	blood:
15	chr1:75200664..75203474-chr1:76250808..76253106,2	K562	blood:
16	chr1:76251691..76252198-chr3:14989937..14990731,2	HCT-116	colon:
17	chr1:76251551..76252348-chr9:32573088..32573673,2	NB4	blood:

No data

Variant related genes	Relation type
RABGGTB	TF binding region
SNORD45A	TF binding region
SNORD45B	TF binding region
SNORD45C	TF binding region
ENSG00000177463	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000113734	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000165264	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000134253	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10873729	0.83[EUR][1000 genomes]
rs10873733	0.81[EUR][1000 genomes]
rs11161598	0.80[EUR][1000 genomes]
rs11161688	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161718	0.88[EUR][1000 genomes]
rs1144340	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146607	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146609	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146610	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146617	0.81[EUR][1000 genomes]
rs1146630	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1146631	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1146634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146635	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146637	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1146639	0.81[EUR][1000 genomes]
rs1146643	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146644	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12092388	0.80[EUR][1000 genomes]
rs12734931	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5745323	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1146632	ENSG00000137955	cis	multi-tissue	Pritchard
rs1146632	MSH4	cis	Artery Tibial	GTEx
rs1146632	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146632	MSH4	cis	Esophagus Muscularis	GTEx
rs1146632	MSH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76249600-76253200	Active TSS	GM12878-XiMat	blood
2	chr1:76250200-76253200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:76250400-76253800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:76250400-76254800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:76250600-76252800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:76250800-76251800	Flanking Active TSS	Dnd41	blood
7	chr1:76250800-76254000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:76251000-76252600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:76251000-76252800	Active TSS	Brain Anterior Caudate	brain
10	chr1:76251000-76252800	Active TSS	Brain Hippocampus Middle	brain
11	chr1:76251000-76252800	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:76251000-76253000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:76251000-76253000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:76251000-76253600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:76251000-76253800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:76251000-76254000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:76251000-76254000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:76251000-76255200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:76251000-76255400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:76251200-76251800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:76251200-76251800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:76251200-76251800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:76251200-76251800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:76251200-76251800	Flanking Active TSS	Fetal Thymus	thymus
25	chr1:76251200-76251800	Flanking Active TSS	HepG2	liver
26	chr1:76251200-76251800	Flanking Active TSS	HMEC	breast
27	chr1:76251200-76251800	Flanking Active TSS	HUVEC	blood vessel
28	chr1:76251200-76252400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:76251200-76252800	Active TSS	Brain Germinal Matrix	brain
30	chr1:76251200-76252800	Active TSS	Brain Substantia Nigra	brain
31	chr1:76251200-76252800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:76251200-76252800	Active TSS	Fetal Lung	lung
33	chr1:76251200-76252800	Active TSS	Rectal Smooth Muscle	rectum
34	chr1:76251200-76253000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr1:76251200-76253000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:76251200-76253000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr1:76251200-76253000	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:76251200-76253000	Active TSS	Colonic Mucosa	Colon
39	chr1:76251200-76253000	Active TSS	Colon Smooth Muscle	Colon
40	chr1:76251200-76253000	Active TSS	Fetal Kidney	kidney
41	chr1:76251200-76253000	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:76251200-76253000	Active TSS	HSMM	muscle
43	chr1:76251200-76253000	Active TSS	Osteobl	bone
44	chr1:76251200-76253200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:76251200-76253200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:76251200-76253200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:76251200-76253200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:76251200-76253200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:76251200-76253200	Active TSS	Thymus	Thymus
50	chr1:76251200-76253200	Active TSS	NH-A	brain

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