Variant report

Variant	rs484416
Chromosome Location	chr1:10491209-10491210
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	CHD2	chr1:10491199-10491399	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:10490008-10491366	GM12878	blood:	n/a	n/a
3	CHD2	chr1:10490179-10491510	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:10490251-10491230	U87	brain:	n/a	n/a
5	UBTF	chr1:10490195-10491528	K562	blood:	n/a	n/a
6	TCF12	chr1:10490139-10491395	ECC-1	luminal epithelium:	n/a	n/a
7	TBL1XR1	chr1:10490105-10491547	K562	blood:	n/a	n/a
8	SIN3AK20	chr1:10490052-10491405	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:10490232-10491258	HEK293	kidney:	n/a	n/a
10	MAX	chr1:10490265-10491360	Hela-S3	cervix:	n/a	n/a
11	ATF2	chr1:10490155-10491320	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAL1	chr1:10490332-10491209	K562	blood:	n/a	n/a
13	POLR2A	chr1:10490195-10491350	Hela-S3	cervix:	n/a	n/a
14	MYC	chr1:10490137-10491213	K562	blood:	n/a	chr1:10490255-10490262
15	E2F4	chr1:10490213-10491409	K562	blood:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
16	POLR2A	chr1:10490083-10491658	HepG2	liver:	n/a	n/a
17	RELA	chr1:10490127-10491544	GM18951	blood:	n/a	n/a
18	MAZ	chr1:10489707-10491577	IMR90	lung:	n/a	chr1:10490255-10490262
19	SMC3	chr1:10489751-10491449	SK-N-SH	brain:	n/a	chr1:10490428-10490438 chr1:10490424-10490438
20	HA-E2F1	chr1:10489950-10491592	MCF-7	breast:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440
21	MYC	chr1:10490146-10491442	NB4	blood:	n/a	chr1:10490255-10490262
22	GTF2F1	chr1:10490221-10491421	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr1:10490029-10491225	GM12878	blood:	n/a	chr1:10490791-10490806
24	RCOR1	chr1:10490250-10491278	HepG2	liver:	n/a	n/a
25	PML	chr1:10490259-10491268	K562	blood:	n/a	n/a
26	MAX	chr1:10490078-10491505	HepG2	liver:	n/a	chr1:10490255-10490262
27	E2F6	chr1:10490010-10491552	H1-hESC	embryonic stem cell:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
28	MAX	chr1:10490019-10491554	H1-hESC	embryonic stem cell:	n/a	chr1:10490255-10490262
29	HCFC1	chr1:10490130-10491307	K562	blood:	n/a	n/a
30	PML	chr1:10489957-10491391	GM12878	blood:	n/a	n/a
31	MXI1	chr1:10489861-10491608	IMR90	lung:	n/a	chr1:10490791-10490806
32	MAZ	chr1:10490258-10491229	Hela-S3	cervix:	n/a	n/a
33	ELF1	chr1:10490172-10491231	GM12878	blood:	n/a	n/a
34	MAX	chr1:10490006-10491361	MCF-7	breast:	n/a	chr1:10490255-10490262
35	CUX1	chr1:10490384-10491319	K562	blood:	n/a	n/a
36	KAP1	chr1:10490267-10491278	U2OS	brain:	n/a	n/a
37	IRF1	chr1:10490164-10491352	K562	blood:	n/a	n/a
38	MAZ	chr1:10490193-10491355	K562	blood:	n/a	chr1:10490255-10490262
39	BRCA1	chr1:10490935-10491285	HepG2	liver:	n/a	n/a
40	MYC	chr1:10490095-10491330	K562	blood:	n/a	chr1:10490255-10490262
41	REST	chr1:10489888-10491538	H1-neurons	neurons:	n/a	chr1:10490770-10490783 chr1:10490697-10490707
42	MTA3	chr1:10489921-10491265	GM12878	blood:	n/a	n/a
43	TAF1	chr1:10490245-10491222	H1-hESC	embryonic stem cell:	n/a	n/a
44	MXI1	chr1:10489950-10491658	SK-N-SH	brain:	n/a	chr1:10490791-10490806
45	GTF3C2	chr1:10490955-10491470	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:10490063-10491434	H1-neurons	neurons:	n/a	n/a
47	NRF1	chr1:10490160-10491561	SK-N-SH	brain:	n/a	chr1:10490749-10490760 chr1:10490748-10490759 chr1:10490749-10490758
48	RAD21	chr1:10489837-10491455	SK-N-SH	brain:	n/a	chr1:10490428-10490438 chr1:10490378-10490388 chr1:10490696-10490709 chr1:10490423-10490442
49	CTCF	chr1:10491200-10491350	AG04449	skin:	n/a	n/a
50	CREB1	chr1:10490051-10491363	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10270585..10272249-chr1:10490197..10491890,2	K562	blood:
2	chr1:10473791..10476777-chr1:10490511..10492354,2	K562	blood:
3	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
4	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
5	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
6	chr1:10490085..10492364-chr1:10508772..10511442,3	K562	blood:
7	chr1:10488905..10491611-chr1:10518532..10520834,2	MCF-7	breast:
8	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
9	chr1:10490864..10493248-chr1:10508230..10510272,2	K562	blood:
10	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
11	chr1:10002273..10004549-chr1:10490535..10492203,2	MCF-7	breast:
12	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

Variant related genes	Relation type
APITD1-CORT	TF binding region
ENSG00000271989	TF binding region
ENSG00000241563	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000203469	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10864455	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864456	0.91[ASN][1000 genomes]
rs1188530	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1307489	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1307490	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1307493	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1307494	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1307497	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1308520	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483686	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2847336	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2847337	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4285702	0.82[ASN][1000 genomes]
rs490037	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs490960	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515423	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544289	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6540931	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs661256	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs661272	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666103	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs676995	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7537164	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944973	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv3373675	chr1:10489565-10491863	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs484416	LZIC	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10489800-10491400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:10489800-10491400	Active TSS	Brain Germinal Matrix	brain
3	chr1:10489800-10491600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:10489800-10491600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:10490000-10491400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:10490000-10491400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:10490000-10491400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:10490000-10491600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:10490000-10491600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:10490000-10491600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr1:10490000-10491600	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr1:10490000-10491600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:10490200-10491400	Active TSS	Ovary	ovary
14	chr1:10490200-10491400	Active TSS	Thymus	Thymus
15	chr1:10490200-10491600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:10490200-10491600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:10490200-10491600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:10490200-10491600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:10490200-10491600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:10490200-10491800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:10490200-10491800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:10490200-10491800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:10490200-10491800	Active TSS	A549	lung
24	chr1:10490400-10491400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:10490400-10491400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:10490400-10491400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:10490400-10491400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:10490400-10491400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:10490400-10491400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:10490400-10491400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:10490400-10491400	Active TSS	Aorta	Aorta
32	chr1:10490400-10491400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:10490400-10491400	Active TSS	Esophagus	oesophagus
34	chr1:10490400-10491400	Active TSS	Fetal Heart	heart
35	chr1:10490400-10491400	Active TSS	Fetal Intestine Large	intestine
36	chr1:10490400-10491400	Active TSS	Fetal Intestine Small	intestine
37	chr1:10490400-10491400	Active TSS	Fetal Lung	lung
38	chr1:10490400-10491400	Active TSS	Fetal Stomach	stomach
39	chr1:10490400-10491400	Active TSS	Gastric	stomach
40	chr1:10490400-10491400	Active TSS	Lung	lung
41	chr1:10490400-10491400	Active TSS	Pancreas	Pancrea
42	chr1:10490400-10491400	Active TSS	Small Intestine	intestine
43	chr1:10490400-10491400	Active TSS	Stomach Mucosa	stomach
44	chr1:10490400-10491400	Active TSS	GM12878-XiMat	blood
45	chr1:10490400-10491400	Active TSS	Hela-S3	cervix
46	chr1:10490400-10491600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr1:10490400-10491600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:10490400-10491600	Active TSS	Fetal Kidney	kidney
49	chr1:10490400-10491600	Active TSS	Left Ventricle	heart
50	chr1:10490400-10491600	Active TSS	Psoas Muscle	Psoas

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