Variant report

Variant	rs721204
Chromosome Location	chr1:76262523-76262524
allele	A/G
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	POLR2A	chr1:76260800-76263815	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	JUND	chr1:76261570-76262865	SK-N-SH	brain:	n/a	n/a
4	MTA3	chr1:76261000-76263232	GM12878	blood:	n/a	n/a
5	HEY1	chr1:76262006-76262767	K562	blood:	n/a	n/a
6	PBX3	chr1:76262216-76262949	A549	lung:	n/a	n/a
7	MAZ	chr1:76262074-76263138	K562	blood:	n/a	chr1:76262981-76262988 chr1:76262979-76262990 chr1:76262980-76262989 chr1:76262980-76262990
8	POLR2A	chr1:76261014-76263954	HEK293	kidney:	n/a	n/a
9	POLR2A	chr1:76260504-76263958	K562	blood:	n/a	n/a
10	BCL3	chr1:76260973-76263369	GM12878	blood:	n/a	n/a
11	ETS1	chr1:76262106-76262762	K562	blood:	n/a	n/a
12	STAT5A	chr1:76261029-76263366	GM12878	blood:	n/a	chr1:76261958-76261966
13	POLR2A	chr1:76257827-76264091	Hela-S3	cervix:	n/a	n/a
14	RUNX3	chr1:76261367-76263183	GM12878	blood:	n/a	n/a
15	MAX	chr1:76262075-76263231	K562	blood:	n/a	chr1:76262981-76262988 chr1:76262979-76262990 chr1:76262980-76262989 chr1:76262980-76262990
16	TAF1	chr1:76262286-76262614	K562	blood:	n/a	n/a
17	POLR2A	chr1:76260673-76263240	A549	lung:	n/a	n/a
18	ZNF274	chr1:76261921-76262772	K562	blood:	n/a	n/a
19	E2F6	chr1:76262178-76263254	K562	blood:	n/a	chr1:76262572-76262583 chr1:76262536-76262545
20	MAZ	chr1:76262506-76262976	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:76262523-76262654	MCF-7	breast:	n/a	n/a
22	POU2F2	chr1:76261459-76263186	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:76261966-76263064	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3AK20	chr1:76262008-76263319	SK-N-SH	brain:	n/a	n/a
25	ZBTB33	chr1:76262115-76262572	K562	blood:	n/a	n/a
26	HMGN3	chr1:76261012-76263063	K562	blood:	n/a	n/a
27	POLR2A	chr1:76260664-76263724	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr1:76261667-76263120	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr1:76262142-76263704	ECC-1	luminal epithelium:	n/a	n/a
30	TEAD4	chr1:76260755-76263209	K562	blood:	n/a	n/a
31	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
32	POLR2A	chr1:76262288-76263050	A549	lung:	n/a	n/a
33	TCF3	chr1:76262484-76262604	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
35	BCL3	chr1:76261105-76263064	K562	blood:	n/a	n/a
36	POLR2A	chr1:76260562-76263803	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:76260648-76263840	PBDE	blood:	n/a	n/a
38	POLR2A	chr1:76261351-76263505	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr1:76260916-76263975	HepG2	liver:	n/a	n/a
40	NFATC1	chr1:76261218-76263336	GM12878	blood:	n/a	n/a
41	ZNF263	chr1:76261536-76263224	HEK293-T-REx	kidney:	n/a	n/a
42	POLR2A	chr1:76260472-76264653	U87	brain:	n/a	n/a
43	BCL3	chr1:76261698-76263192	GM12878	blood:	n/a	n/a
44	ATF2	chr1:76261265-76263025	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
46	NRF1	chr1:76262027-76262690	H1-hESC	embryonic stem cell:	n/a	chr1:76262558-76262569 chr1:76262535-76262546 chr1:76262532-76262546 chr1:76262535-76262546 chr1:76262535-76262549 chr1:76262537-76262546
47	JUND	chr1:76262381-76262912	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr1:76260357-76263709	GM12892	blood:	n/a	n/a
49	POLR2A	chr1:76260821-76263271	K562	blood:	n/a	n/a
50	POLR2A	chr1:76260636-76263660	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:76260266..76263027-chr1:76396916..76399571,2	K562	blood:
2	chr1:76213109..76217378-chr1:76260068..76263795,4	K562	blood:
3	chr1:76208992..76212319-chr1:76261590..76264096,3	K562	blood:
4	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
5	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
6	chr1:76200281..76202966-chr1:76259715..76263170,3	K562	blood:
7	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:

Variant related genes	Relation type
MSH4	TF binding region
ENSG00000117054	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000154007	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001160	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10873797	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11161699	1.00[ASN][1000 genomes]
rs11161848	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164042	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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11579752	0.82[ASN][1000 genomes]
rs11584577	0.94[ASN][1000 genomes]
rs11588643	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1159215	1.00[JPT][hapmap]
rs11810154	0.94[ASN][1000 genomes]
rs12043473	1.00[JPT][hapmap]
rs12118229	0.94[ASN][1000 genomes]
rs12118306	0.94[ASN][1000 genomes]
rs12130832	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12131344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12132750	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12138018	0.82[ASN][1000 genomes]
rs12142247	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1463812	1.00[JPT][hapmap]
rs1498311	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1628063	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs17647178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17647711	0.94[ASN][1000 genomes]
rs1770889	1.00[JPT][hapmap]
rs17848068	0.88[ASN][1000 genomes]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1846233	1.00[CHB][hapmap]
rs1856791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs4403585	0.82[ASN][1000 genomes]
rs4638068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4646960	0.88[ASN][1000 genomes]
rs5745323	1.00[JPT][hapmap]
rs5745325	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5745331	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5745347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5745383	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5745394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs60550898	0.88[ASN][1000 genomes]
rs6593520	1.00[JPT][hapmap]
rs6593521	1.00[JPT][hapmap]
rs6656501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6664254	0.94[ASN][1000 genomes]
rs6675212	0.88[ASN][1000 genomes]
rs6704444	0.88[ASN][1000 genomes]
rs72979226	1.00[ASN][1000 genomes]
rs74090722	0.88[ASN][1000 genomes]
rs74090730	0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs721204	PIGK	cis	parietal	SCAN
rs721204	SNORD45B	cis	parietal	SCAN
rs721204	FAM73A	cis	cerebellum	SCAN
rs721204	ETHE1	trans	lymphoblastoid	seeQTL
rs721204	SNORD45B	cis	cerebellum	SCAN
rs721204	HSPB1	trans	lymphoblastoid	seeQTL
rs721204	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
5	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
8	chr1:76255600-76263000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
11	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:76256000-76262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
17	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
20	chr1:76256200-76262600	Strong transcription	Fetal Kidney	kidney
21	chr1:76256200-76263000	Strong transcription	Ovary	ovary
22	chr1:76256400-76262800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:76256400-76262800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:76256600-76262600	Strong transcription	Primary B cells from cord blood	blood
26	chr1:76256600-76262600	Strong transcription	HMEC	breast
27	chr1:76256600-76263000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:76256600-76263000	Strong transcription	Colon Smooth Muscle	Colon
29	chr1:76256600-76263200	Strong transcription	Brain Angular Gyrus	brain
30	chr1:76256600-76263200	Strong transcription	Rectal Smooth Muscle	rectum
31	chr1:76256600-76263200	Strong transcription	NHLF	lung
32	chr1:76256600-76263400	Strong transcription	Adipose Nuclei	Adipose
33	chr1:76256600-76263400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:76256600-76264000	Strong transcription	Primary hematopoietic stem cells	blood
35	chr1:76256600-76264000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:76256600-76264200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr1:76256600-76264600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:76256800-76263000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:76256800-76263000	Strong transcription	Colonic Mucosa	Colon
41	chr1:76256800-76263200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:76256800-76264000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:76256800-76264200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:76256800-76264200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:76256800-76264200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:76256800-76264400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:76256800-76264600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:76256800-76264800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:76256800-76264800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:76256800-76264800	Strong transcription	Monocytes-CD14+_RO01746	blood

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