Variant report

Variant	rs515423
Chromosome Location	chr1:10485669-10485670
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	FOXA2	chr1:10485326-10485845	A549	lung:	n/a	n/a
2	NR2F2	chr1:10485495-10485732	K562	blood:	n/a	n/a
3	HEY1	chr1:10485638-10486089	HepG2	liver:	n/a	n/a
4	NR2F2	chr1:10485418-10485864	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10474880..10479716-chr1:10481883..10486910,5	K562	blood:

Variant related genes	Relation type
APITD1	TF binding region
APITD1-CORT	TF binding region
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10864455	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864456	0.85[ASN][1000 genomes]
rs1188530	0.83[AMR][1000 genomes]
rs1307489	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1307490	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1307493	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1307494	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1307497	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1308520	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483686	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2847336	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847337	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs484416	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs490037	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs490960	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544289	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6540931	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs661256	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661272	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs666103	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs676995	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7537164	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs944973	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs515423	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
3	chr1:10468800-10489800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:10472000-10490000	Weak transcription	Stomach Mucosa	stomach
5	chr1:10473600-10488000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:10474200-10488000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:10475600-10489600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:10475800-10490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:10477800-10490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:10477800-10490000	Weak transcription	Fetal Heart	heart
11	chr1:10478200-10488000	Weak transcription	Fetal Kidney	kidney
12	chr1:10478200-10490000	Weak transcription	Fetal Brain Male	brain
13	chr1:10478400-10488000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:10479800-10490200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:10480200-10490000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:10480200-10490000	Weak transcription	Pancreas	Pancrea
17	chr1:10480200-10490400	Weak transcription	Aorta	Aorta
18	chr1:10480400-10489600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:10480400-10489800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:10480400-10490000	Weak transcription	Colonic Mucosa	Colon
21	chr1:10480400-10490000	Weak transcription	Small Intestine	intestine
22	chr1:10480400-10490000	Weak transcription	NH-A	brain
23	chr1:10480600-10488000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:10480600-10489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:10480600-10489800	Weak transcription	Hela-S3	cervix
26	chr1:10480800-10486400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:10480800-10487800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:10480800-10488000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:10480800-10488000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:10480800-10488000	Weak transcription	K562	blood
31	chr1:10480800-10489200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:10480800-10489600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:10480800-10489600	Weak transcription	HUVEC	blood vessel
34	chr1:10480800-10490000	Weak transcription	Placenta	Placenta
35	chr1:10480800-10490200	Weak transcription	Left Ventricle	heart
36	chr1:10481000-10488000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:10481000-10489600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:10481000-10489600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:10481000-10489800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:10481000-10490000	Weak transcription	Right Ventricle	heart
41	chr1:10481200-10489600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:10481200-10489800	Weak transcription	Osteobl	bone
43	chr1:10481200-10490000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:10481400-10488000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:10481400-10490200	Weak transcription	Ovary	ovary
46	chr1:10481600-10488000	Weak transcription	GM12878-XiMat	blood
47	chr1:10481600-10488000	Weak transcription	NHEK	skin
48	chr1:10481600-10489800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:10481600-10489800	Weak transcription	HMEC	breast
50	chr1:10481600-10490000	Weak transcription	Gastric	stomach

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