Variant report

Variant	rs4338394
Chromosome Location	chr1:172501000-172501001
allele	G/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	POLR2A	chr1:172500531-172503100	K562	blood:	n/a	n/a
2	TEAD4	chr1:172500605-172503401	K562	blood:	n/a	n/a
3	POLR2A	chr1:172500513-172503382	K562	blood:	n/a	n/a
4	POLR2A	chr1:172500590-172503489	GM12891	blood:	n/a	n/a
5	REST	chr1:172500928-172503498	H1-neurons	neurons:	n/a	chr1:172502117-172502130
6	MXI1	chr1:172500898-172503291	K562	blood:	n/a	n/a
7	SREBP1	chr1:172500153-172503694	GM12878	blood:	n/a	n/a
8	JUND	chr1:172500908-172503242	K562	blood:	n/a	chr1:172502274-172502283 chr1:172502782-172502794
9	MAZ	chr1:172500970-172503418	K562	blood:	n/a	n/a
10	POLR2A	chr1:172500436-172503590	PBDE	blood:	n/a	n/a
11	NRF1	chr1:172500742-172502241	Hela-S3	cervix:	n/a	chr1:172502084-172502095 chr1:172502025-172502034 chr1:172502135-172502144
12	ZNF263	chr1:172500884-172503195	HEK293-T-REx	kidney:	n/a	chr1:172501459-172501468
13	SIN3AK20	chr1:172500362-172503546	MCF-7	breast:	n/a	n/a
14	NR2F2	chr1:172500778-172503430	K562	blood:	n/a	n/a
15	NFYA	chr1:172500657-172502458	Hela-S3	cervix:	n/a	chr1:172502204-172502219 chr1:172501602-172501612 chr1:172501602-172501612 chr1:172501600-172501618 chr1:172502204-172502219
16	GATA1	chr1:172500576-172502919	PBDE	blood:	n/a	chr1:172500762-172500772
17	TBL1XR1	chr1:172500553-172503421	K562	blood:	n/a	n/a
18	POLR2A	chr1:172500880-172503075	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:172500568-172502823	K562	blood:	n/a	n/a
20	MYC	chr1:172500950-172502302	MCF10A-Er-Src	breast:	n/a	n/a
21	JUND	chr1:172500797-172502993	GM12878	blood:	n/a	chr1:172502274-172502283 chr1:172502782-172502794
22	POLR2A	chr1:172500687-172503401	K562	blood:	n/a	n/a
23	MAFK	chr1:172500679-172503256	K562	blood:	n/a	chr1:172501956-172501967
24	POLR2A	chr1:172500959-172503189	HL-60	blood:	n/a	n/a
25	POLR2A	chr1:172500959-172503200	K562	blood:	n/a	n/a
26	HCFC1	chr1:172500408-172504740	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:172500842-172503062	GM12878	blood:	n/a	n/a
28	TAL1	chr1:172500776-172502646	K562	blood:	n/a	n/a
29	POLR2A	chr1:172500782-172502909	K562	blood:	n/a	n/a
30	POLR2A	chr1:172500375-172503329	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr1:172500533-172504004	K562	blood:	n/a	n/a
32	GATA3	chr1:172500280-172501033	SK-N-SH	brain:	n/a	chr1:172500762-172500772
33	CUX1	chr1:172500780-172502034	K562	blood:	n/a	n/a
34	RFX5	chr1:172500645-172503284	Hela-S3	cervix:	n/a	chr1:172501603-172501612
35	TRIM28	chr1:172500796-172502504	K562	blood:	n/a	n/a
36	RCOR1	chr1:172500527-172503380	K562	blood:	n/a	n/a
37	EP300	chr1:172500706-172503615	K562	blood:	n/a	chr1:172500760-172500774 chr1:172502135-172502144
38	MXI1	chr1:172500615-172503731	IMR90	lung:	n/a	n/a
39	ARID3A	chr1:172500629-172502425	K562	blood:	n/a	n/a
40	IRF1	chr1:172500618-172502734	K562	blood:	n/a	chr1:172502697-172502711 chr1:172502008-172502022 chr1:172502101-172502115 chr1:172501580-172501591 chr1:172501579-172501596 chr1:172502208-172502217 chr1:172501602-172501611 chr1:172501579-172501591 chr1:172501576-172501590
41	POLR2A	chr1:172500514-172503184	K562	blood:	n/a	n/a
42	POLR2A	chr1:172500966-172503176	NB4	blood:	n/a	n/a
43	IRF1	chr1:172500475-172503215	K562	blood:	n/a	chr1:172502697-172502711 chr1:172502008-172502022 chr1:172502101-172502115 chr1:172502906-172502915 chr1:172501580-172501591 chr1:172501579-172501596 chr1:172502208-172502217 chr1:172501602-172501611 chr1:172501579-172501591 chr1:172501576-172501590
44	ZNF143	chr1:172500954-172502990	K562	blood:	n/a	chr1:172502025-172502035 chr1:172502135-172502145
45	POLR2A	chr1:172500821-172503466	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
2	chr1:93810767..93811569-chr1:172500955..172501794,2	Hela-S3	cervix:
3	chr1:172486127..172488704-chr1:172497575..172501072,3	MCF-7	breast:
4	chr1:172396812..172398792-chr1:172499531..172501174,2	MCF-7	breast:
5	chr1:172419256..172421468-chr1:172500783..172504604,4	K562	blood:
6	chr1:172499065..172502708-chr1:172575408..172578949,3	K562	blood:
7	chr1:172398685..172401320-chr1:172498374..172501094,2	MCF-7	breast:
8	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:
9	chr1:172480445..172482424-chr1:172499752..172501373,2	K562	blood:
10	chr1:172410326..172414934-chr1:172499314..172504781,7	K562	blood:
11	chr1:172500979..172501763-chrX:16888204..16888920,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-4	chr1:172500900-172502606	NONHSAT007615

Variant related genes	Relation type
SUCO	TF binding region
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000223745	Chromatin interaction
ENSG00000102054	Chromatin interaction
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10218821	0.82[AFR][1000 genomes]
rs12239555	0.87[AFR][1000 genomes]
rs13376238	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1492902	1.00[MEX][hapmap]
rs16844664	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16844666	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16844669	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2422145	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs41533551	0.82[AFR][1000 genomes]
rs4447017	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4500357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6658890	0.82[AFR][1000 genomes]
rs6659546	0.82[AFR][1000 genomes]
rs6667977	0.82[AFR][1000 genomes]
rs73032168	0.81[AMR][1000 genomes]
rs73032170	0.81[AMR][1000 genomes]

No data

Chromatin state (count:163 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172498200-172501200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr1:172499800-172501200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:172500400-172501000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:172500400-172501000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:172500400-172501000	Enhancers	Fetal Intestine Small	intestine
6	chr1:172500400-172501000	Flanking Active TSS	K562	blood
7	chr1:172500400-172501000	Flanking Active TSS	NHLF	lung
8	chr1:172500400-172501400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:172500400-172502400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:172500400-172504600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:172500600-172501000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:172500600-172501000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:172500600-172501000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:172500600-172501000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:172500600-172501000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr1:172500600-172501000	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:172500600-172501000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:172500600-172501000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:172500600-172501000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:172500600-172501000	Active TSS	Fetal Brain Male	brain
21	chr1:172500600-172501000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:172500600-172501000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:172500600-172501000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:172500600-172501000	Enhancers	Spleen	Spleen
25	chr1:172500600-172501000	Flanking Active TSS	GM12878-XiMat	blood
26	chr1:172500600-172501000	Flanking Active TSS	HepG2	liver
27	chr1:172500600-172501000	Flanking Active TSS	HSMM	muscle
28	chr1:172500600-172501000	Flanking Active TSS	NH-A	brain
29	chr1:172500600-172501000	Flanking Active TSS	Osteobl	bone
30	chr1:172500600-172501200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:172500600-172501200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:172500600-172501200	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr1:172500600-172501200	Flanking Active TSS	Fetal Kidney	kidney
34	chr1:172500600-172501200	Flanking Active TSS	Hela-S3	cervix
35	chr1:172500600-172501200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:172500600-172501200	Flanking Active TSS	NHEK	skin
37	chr1:172500600-172501400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:172500600-172501400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:172500600-172501400	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr1:172500600-172501400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:172500600-172501400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:172500600-172503200	Active TSS	Fetal Thymus	thymus
43	chr1:172500600-172503400	Active TSS	Thymus	Thymus
44	chr1:172500600-172503600	Active TSS	A549	lung
45	chr1:172500600-172503800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:172500600-172504200	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:172500600-172504200	Active TSS	NHDF-Ad	bronchial
48	chr1:172500800-172501000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:172500800-172501000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:172500800-172501000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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