Variant report

Variant	rs1146635
Chromosome Location	chr1:76252335-76252336
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	SIN3AK20	chr1:76251494-76252412	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	PML	chr1:76251098-76252684	K562	blood:	n/a	n/a
4	ZNF143	chr1:76251026-76252824	K562	blood:	n/a	n/a
5	BCLAF1	chr1:76251314-76252604	K562	blood:	n/a	chr1:76252354-76252363
6	ZC3H11A	chr1:76251309-76252380	K562	blood:	n/a	n/a
7	MYC	chr1:76250037-76254057	K562	blood:	n/a	chr1:76250221-76250231
8	ZNF384	chr1:76251491-76252497	K562	blood:	n/a	n/a
9	POLR2A	chr1:76251553-76252367	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:76250352-76252499	HCT-116	colon:	n/a	n/a
11	CHD2	chr1:76251655-76252555	GM12878	blood:	n/a	n/a
12	GATA2	chr1:76250970-76252516	SH-SY5Y	brain:	n/a	chr1:76251865-76251874 chr1:76252359-76252372
13	TBP	chr1:76251350-76252806	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:76251046-76252580	GM12892	blood:	n/a	n/a
15	MYC	chr1:76251387-76252551	NB4	blood:	n/a	n/a
16	IRF1	chr1:76250035-76253994	K562	blood:	n/a	chr1:76250222-76250236
17	POLR2A	chr1:76251251-76252353	GM12878	blood:	n/a	n/a
18	MAX	chr1:76251618-76252395	A549	lung:	n/a	n/a
19	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
20	MXI1	chr1:76251277-76252577	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:76251457-76252423	HL-60	blood:	n/a	n/a
22	POLR2A	chr1:76250262-76252896	HCT-116	colon:	n/a	n/a
23	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
24	ELF1	chr1:76251657-76252509	K562	blood:	n/a	chr1:76252354-76252365 chr1:76252355-76252364 chr1:76252354-76252365
25	POLR2A	chr1:76250301-76252545	GM12878	blood:	n/a	n/a
26	ELK1	chr1:76251725-76253119	K562	blood:	n/a	chr1:76252354-76252363 chr1:76252354-76252363
27	TBL1XR1	chr1:76251321-76252458	K562	blood:	n/a	n/a
28	SIN3AK20	chr1:76251380-76252487	HCT-116	colon:	n/a	n/a
29	BCLAF1	chr1:76251584-76252565	GM12878	blood:	n/a	chr1:76252354-76252363
30	MAX	chr1:76251353-76252495	K562	blood:	n/a	n/a
31	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
32	POLR2A	chr1:76251183-76253574	K562	blood:	n/a	n/a
33	STAT3	chr1:76251486-76252344	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr1:76249968-76252912	K562	blood:	n/a	chr1:76250221-76250231
35	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
36	NR2F2	chr1:76251307-76252521	K562	blood:	n/a	n/a
37	MAX	chr1:76251191-76252573	K562	blood:	n/a	n/a
38	CEBPD	chr1:76251290-76252493	K562	blood:	n/a	n/a
39	EP300	chr1:76250272-76252716	GM12878	blood:	n/a	chr1:76252355-76252362
40	POLR2A	chr1:76251238-76252629	GM12891	blood:	n/a	n/a
41	RUNX3	chr1:76251269-76252396	GM12878	blood:	n/a	n/a
42	MAX	chr1:76251243-76252539	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr1:76250173-76253604	GM19193	blood:	n/a	n/a
45	USF1	chr1:76252217-76252566	K562	blood:	n/a	chr1:76252439-76252450
46	CTCF	chr1:76251524-76252649	K562	blood:	n/a	n/a
47	MYBL2	chr1:76251414-76252609	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
49	POLR2A	chr1:76251521-76253603	IMR90	lung:	n/a	n/a
50	STAT3	chr1:76251625-76252496	Hela-S3	cervix:	n/a	chr1:76252351-76252371

No.	Distal block	Cell Line	Cell type
1	chr1:76251676..76252625-chr15:72523942..72524487,2	Hela-S3	cervix:
2	chr1:76189501..76190437-chr1:76251743..76252335,2	NB4	blood:
3	chr1:76190185..76192141-chr1:76251658..76253401,2	MCF-7	breast:
4	chr1:76251477..76252459-chr5:172571057..172571755,2	HCT-116	colon:
5	chr1:76252156..76254487-chr1:76258379..76261694,3	MCF-7	breast:
6	chr1:76251857..76252383-chr1:211555859..211556371,2	Hela-S3	cervix:
7	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
8	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
9	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
10	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
11	chr1:76251016..76253217-chr1:78469296..78471512,3	K562	blood:
12	chr1:75200664..75203474-chr1:76250808..76253106,2	K562	blood:
13	chr1:76251551..76252348-chr9:32573088..32573673,2	NB4	blood:

Variant related genes	Relation type
RABGGTB	TF binding region
SNORD45C	TF binding region
SNORD45A	TF binding region
SNORD45B	TF binding region
ENSG00000067225	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000153363	Chromatin interaction
ENSG00000113734	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000162623	Chromatin interaction
ENSG00000165264	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10873804	0.83[GIH][hapmap]
rs11161602	0.84[MKK][hapmap]
rs11161731	0.86[CEU][hapmap]
rs11161902	1.00[JPT][hapmap]
rs1146632	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146634	0.82[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146636	0.82[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146637	0.81[EUR][1000 genomes]
rs1146639	0.95[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146642	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146644	0.82[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs12024645	0.82[CEU][hapmap];0.81[GIH][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap]
rs12043473	0.84[GIH][hapmap]
rs12132750	1.00[JPT][hapmap]
rs12164500	0.82[CEU][hapmap]
rs12407107	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs12409592	0.84[MKK][hapmap]
rs12410373	0.83[GIH][hapmap]
rs1463812	0.87[GIH][hapmap]
rs211713	0.84[GIH][hapmap]
rs211719	0.84[GIH][hapmap]
rs35290302	0.86[CEU][hapmap];0.89[GIH][hapmap];0.93[MKK][hapmap]
rs3737574	0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[MKK][hapmap]
rs3795251	0.83[GIH][hapmap]
rs3819949	0.81[GIH][hapmap]
rs5745314	0.82[CEU][hapmap]
rs5745334	0.82[CEU][hapmap]
rs5745429	0.86[CEU][hapmap];0.81[GIH][hapmap];0.84[MKK][hapmap]
rs5745448	0.85[GIH][hapmap];0.93[MKK][hapmap]
rs6593520	0.86[GIH][hapmap]
rs6593521	1.00[JPT][hapmap]
rs7525919	0.82[CEU][hapmap]
rs7552289	0.87[GIH][hapmap]
rs814875	0.84[GIH][hapmap]
rs814876	0.84[GIH][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1146635	RABGGTB	cis	cerebellum	SCAN
rs1146635	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146635	ACADM	cis	cerebellum	SCAN
rs1146635	MSH4	cis	Artery Tibial	GTEx
rs1146635	MSH4	cis	parietal	SCAN
rs1146635	MSH4	cis	Muscle Skeletal	GTEx
rs1146635	MSH4	cis	cerebellum	SCAN
rs1146635	ACADM	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr1:76250800-76254000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:76251000-76252600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:76251000-76252800	Active TSS	Brain Anterior Caudate	brain
9	chr1:76251000-76252800	Active TSS	Brain Hippocampus Middle	brain
10	chr1:76251000-76252800	Active TSS	Stomach Smooth Muscle	stomach
11	chr1:76251000-76253000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:76251000-76253000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:76251000-76253600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:76251000-76253800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:76251000-76254000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:76251000-76254000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:76251000-76255200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:76251000-76255400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:76251200-76252400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:76251200-76252800	Active TSS	Brain Germinal Matrix	brain
21	chr1:76251200-76252800	Active TSS	Brain Substantia Nigra	brain
22	chr1:76251200-76252800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:76251200-76252800	Active TSS	Fetal Lung	lung
24	chr1:76251200-76252800	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:76251200-76253000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:76251200-76253000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:76251200-76253000	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:76251200-76253000	Active TSS	Brain Cingulate Gyrus	brain
29	chr1:76251200-76253000	Active TSS	Colonic Mucosa	Colon
30	chr1:76251200-76253000	Active TSS	Colon Smooth Muscle	Colon
31	chr1:76251200-76253000	Active TSS	Fetal Kidney	kidney
32	chr1:76251200-76253000	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:76251200-76253000	Active TSS	HSMM	muscle
34	chr1:76251200-76253000	Active TSS	Osteobl	bone
35	chr1:76251200-76253200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:76251200-76253200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:76251200-76253200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:76251200-76253200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:76251200-76253200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:76251200-76253200	Active TSS	Thymus	Thymus
41	chr1:76251200-76253200	Active TSS	NH-A	brain
42	chr1:76251200-76253400	Active TSS	Brain Angular Gyrus	brain
43	chr1:76251200-76253400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:76251200-76253400	Active TSS	Esophagus	oesophagus
45	chr1:76251200-76253400	Active TSS	Fetal Muscle Trunk	muscle
46	chr1:76251200-76253400	Active TSS	Left Ventricle	heart
47	chr1:76251200-76253400	Active TSS	NHDF-Ad	bronchial
48	chr1:76251200-76253800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:76251200-76253800	Active TSS	Fetal Intestine Small	intestine
50	chr1:76251200-76253800	Active TSS	Fetal Stomach	stomach

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