Variant report

Variant	rs1498311
Chromosome Location	chr1:76254726-76254727
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 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	HEY1	chr1:76254568-76255060	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:76254407-76255532	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr1:76254411-76255312	SK-N-MC	brain:	n/a	n/a
5	NFATC1	chr1:76254451-76255808	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
7	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
9	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:76254651-76254858	Hela-S3	cervix:	n/a	n/a
11	IRF1	chr1:76254387-76254837	K562	blood:	n/a	n/a
12	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
14	NFATC1	chr1:76254333-76255157	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:76254481-76255422	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:76254474-76255273	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:76254725-76255456	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
19	HEY1	chr1:76254472-76255213	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:76254319-76256182	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
23	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
25	CHD1	chr1:76251834-76255268	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:76254473-76255282	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:76254503-76255164	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:76250200-76257400	GM19099	blood:	n/a	n/a
29	POLR2A	chr1:76251210-76255410	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:76254474-76254808	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:76250996-76257615	Hela-S3	cervix:	n/a	n/a
32	RFX5	chr1:76254285-76255559	K562	blood:	n/a	n/a
33	POLR2A	chr1:76251203-76256991	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr1:76250185-76257476	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:76251241-76256430	U87	brain:	n/a	n/a
36	POLR2A	chr1:76254721-76255240	HUVEC	blood vessel:	n/a	n/a
37	CHD1	chr1:76251288-76254995	IMR90	lung:	n/a	n/a
38	POLR2A	chr1:76254477-76255323	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:76252995-76255924	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr1:76251219-76256431	U87	brain:	n/a	n/a
41	POLR2A	chr1:76250036-76255124	K562	blood:	n/a	n/a
42	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
43	POLR2A	chr1:76254448-76255277	K562	blood:	n/a	n/a
44	POLR2A	chr1:76254480-76254818	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr1:76254491-76255346	GM12892	blood:	n/a	n/a
46	POLR2A	chr1:76251015-76255122	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr1:76250199-76255744	HCT-116	colon:	n/a	n/a
48	POLR2A	chr1:76254404-76255519	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr1:76251177-76255478	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr1:76254458-76256363	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
2	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
3	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
4	chr1:76197028..76199654-chr1:76253368..76256114,2	K562	blood:
5	chr1:76213598..76215985-chr1:76254500..76257122,2	K562	blood:
6	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:

No data

Variant related genes	Relation type
SNORD45B	TF binding region
RABGGTB	TF binding region
ENSG00000116791	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000162623	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1001160	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs10873797	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs11161699	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161848	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs11161887	0.84[CEU][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11164042	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1146631	1.00[JPT][hapmap]
rs1146634	1.00[JPT][hapmap]
rs1146636	1.00[JPT][hapmap]
rs1146644	1.00[JPT][hapmap]
rs11578480	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579752	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11584577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588643	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];0.95[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]
rs1159215	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs11810154	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043473	1.00[JPT][hapmap]
rs12118229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12118306	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130832	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12131344	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12132750	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12138018	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12142247	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12145870	0.84[EUR][1000 genomes]
rs1250876	0.84[CEU][hapmap]
rs1250880	0.81[CEU][hapmap]
rs1303870	0.84[CEU][hapmap]
rs1463812	1.00[JPT][hapmap]
rs1628063	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs1630587	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1689270	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17647178	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17647711	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1770889	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17848068	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796813	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1796815	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1796827	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1846233	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1856791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1908089	0.84[CEU][hapmap]
rs2029682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4403585	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4638068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4646960	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745323	1.00[JPT][hapmap]
rs5745325	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5745430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745523	0.84[CEU][hapmap]
rs5745543	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5745545	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5745546	0.84[CEU][hapmap]
rs5745547	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs60550898	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593520	1.00[JPT][hapmap]
rs6593521	1.00[JPT][hapmap]
rs6656501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664254	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675212	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6704444	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721204	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72979226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74090722	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74090730	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7516477	0.84[CEU][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1498311	TFDP2	trans	lymphoblastoid	seeQTL
rs1498311	FAM73A	cis	cerebellum	SCAN
rs1498311	SNORD45B	cis	cerebellum	SCAN
rs1498311	PIGK	cis	parietal	SCAN
rs1498311	SNORD45B	cis	parietal	SCAN
rs1498311	RPS6KA4	trans	parietal	SCAN
rs1498311	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76250400-76254800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:76251000-76255200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:76251000-76255400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:76251200-76255000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:76251200-76255000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:76251200-76255400	Active TSS	Right Atrium	heart
7	chr1:76251200-76256200	Active TSS	Right Ventricle	heart
8	chr1:76251400-76254800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:76251600-76254800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:76251600-76254800	Active TSS	NHLF	lung
11	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
12	chr1:76252400-76255200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
14	chr1:76252600-76254800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:76252600-76257600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:76252800-76254800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:76252800-76254800	Flanking Active TSS	Liver	Liver
18	chr1:76252800-76255000	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:76252800-76255200	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr1:76252800-76256000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
21	chr1:76252800-76256800	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr1:76252800-76257000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
23	chr1:76252800-76257000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:76252800-76257200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
25	chr1:76253000-76255200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
26	chr1:76253000-76255200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:76253000-76255400	Transcr. at gene 5' and 3'	HSMM	muscle
28	chr1:76253000-76255600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:76253000-76255800	Transcr. at gene 5' and 3'	HMEC	breast
30	chr1:76253000-76256000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
31	chr1:76253000-76256800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
32	chr1:76253000-76257400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
33	chr1:76253200-76255200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:76253200-76255200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr1:76253200-76255200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:76253200-76255200	Transcr. at gene 5' and 3'	Osteobl	bone
37	chr1:76253200-76256000	Transcr. at gene 5' and 3'	NH-A	brain
38	chr1:76253200-76256600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:76253200-76256600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:76253200-76257400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:76253400-76254800	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
42	chr1:76253400-76255000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:76253400-76255000	Active TSS	HepG2	liver
44	chr1:76253400-76255000	Flanking Active TSS	HUVEC	blood vessel
45	chr1:76253400-76255400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:76253400-76255400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
47	chr1:76253400-76256800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:76253600-76255800	Enhancers	Brain Substantia Nigra	brain
49	chr1:76253600-76256200	Weak transcription	Esophagus	oesophagus
50	chr1:76253600-76256800	Genic enhancers	Primary monocytes fromperipheralblood	blood

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