Variant report

Variant	rs1146631
Chromosome Location	chr1:76250636-76250637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:134)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:134 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76250272-76250788	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	MYC	chr1:76250037-76254057	K562	blood:	n/a	chr1:76250221-76250231
4	CEBPD	chr1:76250077-76250810	K562	blood:	n/a	n/a
5	POLR2A	chr1:76250352-76252499	HCT-116	colon:	n/a	n/a
6	POLR2A	chr1:76250280-76250977	GM12891	blood:	n/a	n/a
7	TRIM28	chr1:76249909-76250982	K562	blood:	n/a	n/a
8	STAT5A	chr1:76250327-76250717	GM12878	blood:	n/a	n/a
9	SP1	chr1:76250265-76250805	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:76250321-76251063	GM12878	blood:	n/a	n/a
11	POU2F2	chr1:76250251-76250709	GM12878	blood:	n/a	n/a
12	MAZ	chr1:76250004-76250779	GM12878	blood:	n/a	chr1:76250221-76250231
13	IRF1	chr1:76250035-76253994	K562	blood:	n/a	chr1:76250222-76250236
14	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
15	POLR2A	chr1:76250262-76252896	HCT-116	colon:	n/a	n/a
16	TBL1XR1	chr1:76250322-76250732	K562	blood:	n/a	n/a
17	MYC	chr1:76250196-76250756	NB4	blood:	n/a	chr1:76250221-76250231
18	MXI1	chr1:76250023-76251017	GM12878	blood:	n/a	n/a
19	TAF1	chr1:76250243-76251039	K562	blood:	n/a	n/a
20	POLR2A	chr1:76250301-76252545	GM12878	blood:	n/a	n/a
21	RCOR1	chr1:76250275-76250715	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:76250280-76251017	GM12892	blood:	n/a	n/a
23	BHLHE40	chr1:76250036-76250902	GM12878	blood:	n/a	n/a
24	MXI1	chr1:76250247-76250669	K562	blood:	n/a	n/a
25	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
26	NR2F2	chr1:76250080-76250650	K562	blood:	n/a	n/a
27	CEBPB	chr1:76250403-76250675	K562	blood:	n/a	n/a
28	YY1	chr1:76250322-76250898	K562	blood:	n/a	n/a
29	POLR2A	chr1:76250251-76251003	GM12878	blood:	n/a	n/a
30	MYC	chr1:76249968-76252912	K562	blood:	n/a	chr1:76250221-76250231
31	RCOR1	chr1:76249739-76251031	K562	blood:	n/a	n/a
32	YY1	chr1:76250284-76250797	GM12878	blood:	n/a	n/a
33	EP300	chr1:76250272-76252716	GM12878	blood:	n/a	chr1:76252355-76252362
34	PAX5	chr1:76250347-76250912	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:76250173-76253604	GM19193	blood:	n/a	n/a
36	MAX	chr1:76250157-76251004	GM12878	blood:	n/a	chr1:76250221-76250231
37	TBL1XR1	chr1:76250366-76250711	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:76250302-76250924	GM12891	blood:	n/a	n/a
39	RUNX3	chr1:76249931-76250901	GM12878	blood:	n/a	n/a
40	PML	chr1:76250116-76253155	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:76250200-76254234	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:76250130-76254424	K562	blood:	n/a	n/a
43	POLR2A	chr1:76250030-76252695	GM15510	blood:	n/a	n/a
44	FOXM1	chr1:76250311-76250811	GM12878	blood:	n/a	n/a
45	MAFK	chr1:76250309-76250727	K562	blood:	n/a	n/a
46	ATF2	chr1:76250293-76250672	GM12878	blood:	n/a	n/a
47	SPI1	chr1:76250260-76250721	HL-60	blood:	n/a	n/a
48	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
49	TAL1	chr1:76250057-76250661	K562	blood:	n/a	n/a
50	POLR2A	chr1:76250277-76254427	GM12892	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76208509..76211228-chr1:76250454..76252141,2	K562	blood:
2	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
3	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
4	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
5	chr1:76080033..76082466-chr1:76250224..76251859,2	MCF-7	breast:
6	chr1:76213297..76216875-chr1:76250212..76251937,3	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
ENSG00000117054	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873729	0.81[EUR][1000 genomes]
rs10873733	0.81[EUR][1000 genomes]
rs10873797	1.00[JPT][hapmap]
rs11161598	0.82[EUR][1000 genomes]
rs11161688	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161718	0.87[EUR][1000 genomes]
rs11161848	1.00[JPT][hapmap]
rs11163967	1.00[JPT][hapmap]
rs1144340	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146591	1.00[JPT][hapmap]
rs1146598	0.80[EUR][1000 genomes]
rs1146607	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146609	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146610	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1146617	0.82[EUR][1000 genomes]
rs1146630	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1146634	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]
rs1146636	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]
rs1146637	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146642	0.82[CEU][hapmap]
rs1146643	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146644	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12043473	1.00[JPT][hapmap]
rs12092388	0.82[EUR][1000 genomes]
rs12130832	1.00[JPT][hapmap]
rs12131344	1.00[JPT][hapmap]
rs12132750	1.00[CHB][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12726486	1.00[JPT][hapmap]
rs12731627	1.00[JPT][hapmap]
rs12733990	1.00[JPT][hapmap]
rs12734931	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743235	1.00[JPT][hapmap]
rs1463812	1.00[JPT][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]
rs4638068	1.00[JPT][hapmap]
rs5745317	1.00[JPT][hapmap]
rs5745323	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745352	1.00[JPT][hapmap]
rs5745368	1.00[JPT][hapmap]
rs5745376	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745391	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745403	1.00[JPT][hapmap]
rs5745425	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745434	1.00[JPT][hapmap]
rs5745438	1.00[JPT][hapmap]
rs5745537	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs5745549	1.00[JPT][hapmap]
rs6593520	1.00[JPT][hapmap]
rs6656501	1.00[JPT][hapmap]
rs721204	1.00[JPT][hapmap]

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	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	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1146631	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146631	MSH4	cis	Muscle Skeletal	GTEx
rs1146631	MSH4	cis	Artery Tibial	GTEx
rs1146631	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76241400-76251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:76241400-76251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:76244400-76250800	Weak transcription	HepG2	liver
4	chr1:76249200-76251200	Weak transcription	Right Atrium	heart
5	chr1:76249600-76253200	Active TSS	GM12878-XiMat	blood
6	chr1:76249800-76251000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:76249800-76251200	Active TSS	K562	blood
8	chr1:76250000-76250800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr1:76250000-76250800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:76250000-76250800	Active TSS	Dnd41	blood
11	chr1:76250000-76251000	Active TSS	Primary T cells from cord blood	blood
12	chr1:76250200-76250800	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr1:76250200-76251000	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:76250200-76251000	Active TSS	Duodenum Mucosa	Duodenum
15	chr1:76250200-76251600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr1:76250200-76253200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr1:76250400-76250800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr1:76250400-76250800	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:76250400-76251000	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr1:76250400-76251200	Enhancers	Fetal Thymus	thymus
21	chr1:76250400-76253800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:76250400-76254800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:76250600-76251000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:76250600-76251000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:76250600-76251000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:76250600-76251000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:76250600-76251200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:76250600-76251200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:76250600-76251600	Flanking Active TSS	Placenta	Placenta
30	chr1:76250600-76252800	Active TSS	HUES6 Cell Line	embryonic stem cell

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