Variant report

Variant	rs904327
Chromosome Location	chr1:220263074-220263075
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	chr1:220262992-220263192	A549	lung:	n/a	n/a
2	POLR2A	chr1:220262882-220263470	HepG2	liver:	n/a	n/a
3	CEBPB	chr1:220263017-220263464	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:220262847-220263878	GM12892	blood:	n/a	n/a
5	TAF1	chr1:220262934-220263324	Hela-S3	cervix:	n/a	n/a
6	EP300	chr1:220262926-220263567	GM12878	blood:	n/a	chr1:220263346-220263360
7	POLR2A	chr1:220262908-220263307	HUVEC	blood vessel:	n/a	n/a
8	CUX1	chr1:220262800-220263452	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:220262876-220263447	K562	blood:	n/a	n/a
10	JUND	chr1:220262799-220263619	T-47D	breast:	n/a	chr1:220263251-220263265
11	MAX	chr1:220262740-220263621	A549	lung:	n/a	n/a
12	CHD2	chr1:220262948-220263428	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:220262891-220263380	HUVEC	blood vessel:	n/a	n/a
14	NRF1	chr1:220263004-220263429	GM12878	blood:	n/a	chr1:220263187-220263196 chr1:220263187-220263198 chr1:220263187-220263201 chr1:220263184-220263198 chr1:220263186-220263197
15	ATF3	chr1:220262929-220263522	A549	lung:	n/a	n/a
16	POLR2A	chr1:220262415-220263869	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:220262888-220263559	HepG2	liver:	n/a	n/a
18	RCOR1	chr1:220262819-220263604	GM12878	blood:	n/a	n/a
19	SIN3A	chr1:220262955-220263447	GM12878	blood:	n/a	n/a
20	MAFK	chr1:220262964-220263427	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr1:220262900-220263404	H1-hESC	embryonic stem cell:	n/a	n/a
22	MBD4	chr1:220262764-220263486	HepG2	liver:	n/a	n/a
23	YY1	chr1:220263074-220263327	HCT-116	colon:	n/a	n/a
24	CEBPB	chr1:220263043-220263414	HepG2	liver:	n/a	n/a
25	SP1	chr1:220262725-220263641	A549	lung:	n/a	n/a
26	NFIC	chr1:220262921-220263441	HepG2	liver:	n/a	n/a
27	YY1	chr1:220262905-220263442	GM12878	blood:	n/a	n/a
28	GTF2F1	chr1:220262985-220263430	Hela-S3	cervix:	n/a	n/a
29	SIX5	chr1:220263031-220263375	A549	lung:	n/a	n/a
30	USF1	chr1:220263023-220263474	SK-N-SH	brain:	n/a	n/a
31	TAF1	chr1:220262943-220263328	HepG2	liver:	n/a	n/a
32	GATA2	chr1:220262864-220263846	SH-SY5Y	brain:	n/a	n/a
33	FOXA2	chr1:220262856-220263408	A549	lung:	n/a	n/a
34	TBL1XR1	chr1:220262724-220263669	K562	blood:	n/a	n/a
35	MAX	chr1:220262899-220263523	SK-N-SH	brain:	n/a	n/a
36	RFX5	chr1:220262918-220263480	Hela-S3	cervix:	n/a	n/a
37	MAX	chr1:220262810-220263527	A549	lung:	n/a	n/a
38	YY1	chr1:220262955-220263376	GM12878	blood:	n/a	n/a
39	MAX	chr1:220262939-220264019	K562	blood:	n/a	n/a
40	USF1	chr1:220263007-220263564	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:220262981-220263420	H1-neurons	neurons:	n/a	n/a
42	NFIC	chr1:220262921-220263637	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:220262945-220263221	SK-N-SH	brain:	n/a	n/a
44	CREB1	chr1:220262853-220263633	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:220262878-220263577	GM12878	blood:	n/a	n/a
46	GABPA	chr1:220262911-220263490	A549	lung:	n/a	chr1:220263187-220263196 chr1:220263187-220263198 chr1:220263187-220263201 chr1:220263184-220263198
47	MAZ	chr1:220262842-220264029	K562	blood:	n/a	n/a
48	E2F6	chr1:220263055-220263292	K562	blood:	n/a	chr1:220263176-220263183 chr1:220263235-220263249 chr1:220263176-220263183 chr1:220263238-220263245 chr1:220263188-220263197 chr1:220263176-220263183 chr1:220263238-220263245 chr1:220263238-220263245
49	GRp20	chr1:220263069-220263391	HepG2	liver:	n/a	n/a
50	SP1	chr1:220262853-220263541	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220219521..220220100-chr1:220262803..220263613,2	K562	blood:
2	chr1:220260533..220264899-chr1:220265232..220269626,12	MCF-7	breast:
3	chr1:220218169..220221765-chr1:220261064..220269153,11	MCF-7	breast:
4	chr1:220262657..220263213-chr16:28834391..28835257,2	Hela-S3	cervix:
5	chr1:220261171..220264758-chr1:220266195..220270505,9	MCF-7	breast:
6	chr1:220218207..220221672-chr1:220261461..220265020,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPRS-2	chr1:220263028-220263191	NONHSAT009576

Variant related genes	Relation type
IARS2	TF binding region
ENSG00000067704	Chromatin interaction
ENSG00000136628	Chromatin interaction
ENSG00000168488	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11118488	1.00[MEX][hapmap]
rs11800305	1.00[MEX][hapmap]
rs11807333	1.00[MEX][hapmap]
rs1611863	0.82[AFR][1000 genomes]
rs2577135	0.84[AFR][1000 genomes]
rs2577153	1.00[AMR][1000 genomes]
rs2647471	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2647472	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes]
rs2789785	1.00[ASW][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs2889877	1.00[MEX][hapmap]
rs7524161	0.84[AFR][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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220238000-220267400	Weak transcription	Spleen	Spleen
2	chr1:220261800-220263800	Active TSS	Hela-S3	cervix
3	chr1:220261800-220263800	Active TSS	HSMM	muscle
4	chr1:220261800-220264000	Active TSS	A549	lung
5	chr1:220261800-220264200	Active TSS	K562	blood
6	chr1:220262000-220263200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:220262000-220263600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:220262000-220263600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:220262000-220263600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:220262000-220263800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:220262000-220263800	Active TSS	Brain Germinal Matrix	brain
12	chr1:220262000-220263800	Active TSS	Brain Hippocampus Middle	brain
13	chr1:220262000-220263800	Active TSS	GM12878-XiMat	blood
14	chr1:220262000-220264000	Active TSS	Duodenum Mucosa	Duodenum
15	chr1:220262000-220264000	Active TSS	HMEC	breast
16	chr1:220262200-220263400	Active TSS	Dnd41	blood
17	chr1:220262200-220264000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:220262400-220263200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr1:220262400-220263200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr1:220262400-220263400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr1:220262400-220263400	Active TSS	Fetal Muscle Trunk	muscle
22	chr1:220262400-220263400	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr1:220262400-220263400	Active TSS	HUVEC	blood vessel
24	chr1:220262400-220263400	Active TSS	Osteobl	bone
25	chr1:220262400-220263600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:220262400-220263600	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:220262400-220263600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:220262400-220263600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:220262400-220263600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:220262400-220263600	Active TSS	Aorta	Aorta
31	chr1:220262400-220263600	Active TSS	Brain Substantia Nigra	brain
32	chr1:220262400-220263600	Active TSS	Fetal Lung	lung
33	chr1:220262400-220263600	Active TSS	Placenta	Placenta
34	chr1:220262400-220263600	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:220262400-220263600	Active TSS	NHLF	lung
36	chr1:220262400-220263800	Active TSS	H1 Cell Line	embryonic stem cell
37	chr1:220262400-220263800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:220262400-220263800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:220262400-220263800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:220262400-220263800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:220262400-220263800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:220262400-220263800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:220262400-220263800	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr1:220262400-220263800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:220262400-220263800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:220262400-220263800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:220262400-220263800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:220262400-220263800	Active TSS	Fetal Brain Female	brain
49	chr1:220262400-220263800	Active TSS	Fetal Intestine Small	intestine
50	chr1:220262400-220263800	Active TSS	Fetal Kidney	kidney

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