Variant report

Variant	rs1146636
Chromosome Location	chr1:76252687-76252688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	ZNF143	chr1:76251026-76252824	K562	blood:	n/a	n/a
3	POLR2A	chr1:76252627-76253022	ProgFib	skin:	n/a	n/a
4	MYC	chr1:76250037-76254057	K562	blood:	n/a	chr1:76250221-76250231
5	TBP	chr1:76251350-76252806	Hela-S3	cervix:	n/a	n/a
6	IRF1	chr1:76250035-76253994	K562	blood:	n/a	chr1:76250222-76250236
7	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
8	POLR2A	chr1:76250262-76252896	HCT-116	colon:	n/a	n/a
9	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
10	ELK1	chr1:76251725-76253119	K562	blood:	n/a	chr1:76252354-76252363 chr1:76252354-76252363
11	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
12	POLR2A	chr1:76251183-76253574	K562	blood:	n/a	n/a
13	MYC	chr1:76249968-76252912	K562	blood:	n/a	chr1:76250221-76250231
14	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
15	CUX1	chr1:76252654-76252854	GM12878	blood:	n/a	n/a
16	EP300	chr1:76250272-76252716	GM12878	blood:	n/a	chr1:76252355-76252362
17	POLR2A	chr1:76252629-76253298	GM12891	blood:	n/a	n/a
18	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:76250173-76253604	GM19193	blood:	n/a	n/a
20	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
21	POLR2A	chr1:76251521-76253603	IMR90	lung:	n/a	n/a
22	PML	chr1:76250116-76253155	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:76250200-76254234	GM12878	blood:	n/a	n/a
24	BHLHE40	chr1:76251499-76252706	K562	blood:	n/a	n/a
25	POLR2A	chr1:76252662-76252974	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:76250130-76254424	K562	blood:	n/a	n/a
27	POLR2A	chr1:76250030-76252695	GM15510	blood:	n/a	n/a
28	CEBPB	chr1:76251479-76252965	K562	blood:	n/a	n/a
29	POLR2A	chr1:76251041-76254344	GM12892	blood:	n/a	n/a
30	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:76250277-76254427	GM12892	blood:	n/a	n/a
32	MXI1	chr1:76251558-76253248	K562	blood:	n/a	n/a
33	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:76250028-76253609	K562	blood:	n/a	n/a
35	POLR2A	chr1:76251241-76254471	HUVEC	blood vessel:	n/a	n/a
36	HEY1	chr1:76251063-76252819	HepG2	liver:	n/a	n/a
37	SPI1	chr1:76252203-76252705	HL-60	blood:	n/a	n/a
38	POLR2A	chr1:76249915-76253627	Raji	blood:	n/a	n/a
39	HCFC1	chr1:76251135-76253681	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:76251264-76252963	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
42	POLR2A	chr1:76250320-76254265	GM18526	blood:	n/a	n/a
43	MYC	chr1:76251372-76253027	K562	blood:	n/a	n/a
44	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
45	TBL1XR1	chr1:76249814-76254171	K562	blood:	n/a	n/a
46	TEAD4	chr1:76251158-76252738	K562	blood:	n/a	n/a
47	POLR2A	chr1:76251379-76253969	HepG2	liver:	n/a	n/a
48	MAFK	chr1:76252591-76252843	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
50	FOXM1	chr1:76251263-76252718	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76190185..76192141-chr1:76251658..76253401,2	MCF-7	breast:
2	chr1:76252156..76254487-chr1:76258379..76261694,3	MCF-7	breast:
3	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
4	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
5	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
6	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
7	chr1:76251016..76253217-chr1:78469296..78471512,3	K562	blood:
8	chr1:75200664..75203474-chr1:76250808..76253106,2	K562	blood:

No data

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

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873729	0.83[EUR][1000 genomes]
rs10873733	0.81[EUR][1000 genomes]
rs10873797	1.00[JPT][hapmap]
rs11161598	0.80[EUR][1000 genomes]
rs11161688	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161718	0.88[EUR][1000 genomes]
rs11161848	1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[JPT][hapmap]
rs1144340	0.89[EUR][1000 genomes];1.00[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]
rs1146631	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146635	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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146639	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1146642	0.83[CEU][hapmap]
rs1146643	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12043473	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12092388	0.80[EUR][1000 genomes]
rs12130832	1.00[JPT][hapmap]
rs12131344	1.00[JPT][hapmap]
rs12132750	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12734931	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463812	0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1498311	1.00[JPT][hapmap]
rs1628063	1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs17647178	1.00[JPT][hapmap]
rs1770889	1.00[JPT][hapmap]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1856791	1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs211713	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs211719	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs35290302	0.83[GIH][hapmap]
rs3737574	0.83[GIH][hapmap]
rs4638068	1.00[JPT][hapmap]
rs5745323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs6593520	0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs6593521	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6656501	1.00[JPT][hapmap]
rs721204	1.00[JPT][hapmap]
rs7552289	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs814875	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs814876	0.91[GIH][hapmap];0.83[TSI][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1146636	RABGGTB	cis	cerebellum	SCAN
rs1146636	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146636	RABGGTB	cis	lymphoblastoid	seeQTL
rs1146636	RABGGTB	cis	parietal	SCAN
rs1146636	MSH4	cis	cerebellum	SCAN
rs1146636	MSH4	cis	Esophagus Muscularis	GTEx
rs1146636	MSH4	cis	parietal	SCAN
rs1146636	MSH4	cis	Muscle Skeletal	GTEx
rs1146636	ACADM	cis	cerebellum	SCAN
rs1146636	MSH4	cis	Artery Tibial	GTEx

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

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