Variant report

Variant	rs10450662
Chromosome Location	chr11:71159640-71159641
allele	C/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	SP2	chr11:71159341-71159781	HepG2	liver:	n/a	chr11:71159484-71159499
2	USF1	chr11:71159321-71159844	K562	blood:	n/a	chr11:71159577-71159593
3	MYC	chr11:71158283-71160560	NB4	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
4	MXI1	chr11:71158902-71160350	HepG2	liver:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
5	SP4	chr11:71159218-71159889	H1-hESC	embryonic stem cell:	n/a	chr11:71159488-71159499
6	CREB1	chr11:71159167-71160243	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr11:71159332-71160255	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
8	TCF12	chr11:71159117-71160029	ECC-1	luminal epithelium:	n/a	chr11:71159170-71159180
9	ATF1	chr11:71159298-71159956	K562	blood:	n/a	n/a
10	ZC3H11A	chr11:71159552-71159749	K562	blood:	n/a	n/a
11	IRF3	chr11:71159393-71159661	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:71159194-71160175	GM12891	blood:	n/a	n/a
13	POLR2A	chr11:71158476-71160220	MCF-7	breast:	n/a	n/a
14	POLR2A	chr11:71159175-71159915	PANC-1	pancreas:	n/a	n/a
15	MAX	chr11:71158758-71160290	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
16	MXI1	chr11:71159306-71160648	K562	blood:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
17	ZKSCAN1	chr11:71159271-71160115	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:71159052-71159997	GM12892	blood:	n/a	n/a
19	EP300	chr11:71159076-71160066	ECC-1	luminal epithelium:	n/a	chr11:71159563-71159572
20	FOS	chr11:71159309-71159751	K562	blood:	n/a	chr11:71159482-71159491 chr11:71159426-71159436 chr11:71159426-71159436
21	POLR2A	chr11:71158961-71160268	H1-hESC	embryonic stem cell:	n/a	n/a
22	SIN3AK20	chr11:71159527-71159867	K562	blood:	n/a	n/a
23	USF1	chr11:71159593-71159850	HepG2	liver:	n/a	n/a
24	BHLHE40	chr11:71159278-71159865	GM12878	blood:	n/a	chr11:71159577-71159593
25	MYC	chr11:71159212-71160229	MCF-7	breast:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
26	MAZ	chr11:71158939-71160276	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
27	EP300	chr11:71159465-71159844	GM12878	blood:	n/a	chr11:71159563-71159572
28	MYC	chr11:71159083-71160272	MCF-7	breast:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
29	SP1	chr11:71159128-71159934	H1-hESC	embryonic stem cell:	n/a	chr11:71159697-71159709 chr11:71159449-71159461 chr11:71159703-71159713 chr11:71159151-71159165 chr11:71159150-71159162 chr11:71159694-71159708 chr11:71159516-71159537 chr11:71159449-71159461 chr11:71159698-71159707 chr11:71159150-71159162 chr11:71159152-71159161 chr11:71159703-71159713 chr11:71159488-71159499 chr11:71159451-71159460 chr11:71159145-71159157 chr11:71159698-71159708 chr11:71159151-71159160 chr11:71159698-71159708 chr11:71159699-71159708 chr11:71159697-71159709 chr11:71159227-71159241
30	EGR1	chr11:71159282-71159816	K562	blood:	n/a	chr11:71159646-71159661 chr11:71159452-71159465 chr11:71159694-71159708 chr11:71159652-71159662 chr11:71159449-71159463
31	MXI1	chr11:71159325-71160501	Hela-S3	cervix:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
32	USF1	chr11:71159377-71160017	GM12878	blood:	n/a	chr11:71159577-71159593
33	TAF1	chr11:71159150-71159998	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr11:71159062-71159844	ProgFib	skin:	n/a	n/a
35	E2F4	chr11:71159328-71159787	MCF10A-Er-Src	breast:	n/a	chr11:71159527-71159536 chr11:71159563-71159572 chr11:71159451-71159460
36	ZBTB7A	chr11:71159148-71159887	K562	blood:	n/a	chr11:71159649-71159660
37	SREBP1	chr11:71158815-71159825	HepG2	liver:	n/a	n/a
38	MXI1	chr11:71158924-71160266	GM12878	blood:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
39	NFYB	chr11:71159212-71160079	Hela-S3	cervix:	n/a	chr11:71159525-71159540 chr11:71159527-71159539 chr11:71159523-71159538 chr11:71159523-71159538 chr11:71159478-71159492
40	POLR2A	chr11:71159230-71159928	MCF10A-Er-Src	breast:	n/a	n/a
41	SIN3AK20	chr11:71159552-71160183	PANC-1	pancreas:	n/a	n/a
42	MYC	chr11:71159254-71160212	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
43	HMGN3	chr11:71158801-71160243	K562	blood:	n/a	n/a
44	POLR2A	chr11:71159558-71159880	HepG2	liver:	n/a	n/a
45	FOSL2	chr11:71159163-71159792	HepG2	liver:	n/a	chr11:71159482-71159491 chr11:71159426-71159436 chr11:71159426-71159436
46	MAX	chr11:71158768-71160515	HCT-116	colon:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
47	CTCF	chr11:71159628-71159656	Spleen_OC	spleen:	n/a	n/a
48	POLR2A	chr11:71159133-71159870	HCT-116	colon:	n/a	n/a
49	RELA	chr11:71159237-71160301	GM18951	blood:	n/a	n/a
50	POLR2A	chr11:71158831-71160228	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71158745..71161047-chr14:24656517..24659263,2	MCF-7	breast:
2	chr11:71159548..71160234-chr19:19029798..19030317,2	Hela-S3	cervix:
3	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
4	chr11:70805722..70807297-chr11:71158455..71160766,2	MCF-7	breast:
5	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
6	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NADSYN1-1	chr11:71159586-71159931	XLOC_009199
2	lnc-NADSYN1-1	chr11:71159587-71159931	NONHSAT022678

Variant related genes	Relation type
ENSG00000254682	TF binding region
DHCR7	TF binding region
NADSYN1	TF binding region
ENSG00000172893	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000162105	Chromatin interaction
ENSG00000204572	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000172890	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10450661	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12270619	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12280295	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12284909	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12286997	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17161531	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59601821	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7950991	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 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	chr11:71158000-71161000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:71158000-71161000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:71158200-71160200	Active TSS	HSMMtube	muscle
4	chr11:71158400-71160000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:71158400-71160200	Bivalent/Poised TSS	HepG2	liver
6	chr11:71158400-71160400	Active TSS	HSMM	muscle
7	chr11:71158400-71160600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:71158400-71160600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr11:71158400-71160800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:71158400-71160800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:71158400-71160800	Active TSS	Rectal Smooth Muscle	rectum
12	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:71158400-71161400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:71158600-71159800	Active TSS	Esophagus	oesophagus
16	chr11:71158600-71160000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr11:71158600-71160400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr11:71158600-71160400	Active TSS	Gastric	stomach
19	chr11:71158600-71160400	Active TSS	A549	lung
20	chr11:71158600-71160600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr11:71158600-71160800	Active TSS	Fetal Kidney	kidney
22	chr11:71158600-71160800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr11:71158600-71160800	Active TSS	Lung	lung
24	chr11:71158600-71160800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr11:71158600-71160800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr11:71158600-71161000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr11:71158600-71161000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr11:71158600-71161200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr11:71158600-71161200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:71158600-71161200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr11:71158600-71161200	Active TSS	HMEC	breast
32	chr11:71158600-71161400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr11:71158800-71159800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:71158800-71159800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:71158800-71160000	Active TSS	Fetal Brain Female	brain
36	chr11:71158800-71160000	Active TSS	Placenta Amnion	Placenta Amnion
37	chr11:71158800-71160000	Active TSS	Psoas Muscle	Psoas
38	chr11:71158800-71160000	Active TSS	NHEK	skin
39	chr11:71158800-71160200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:71158800-71160200	Active TSS	Brain Cingulate Gyrus	brain
41	chr11:71158800-71160400	Active TSS	Small Intestine	intestine
42	chr11:71158800-71160600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:71158800-71160600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr11:71158800-71160600	Active TSS	Fetal Brain Male	brain
45	chr11:71158800-71160600	Active TSS	Ovary	ovary
46	chr11:71158800-71160600	Active TSS	Right Ventricle	heart
47	chr11:71158800-71160600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr11:71158800-71160800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:71158800-71160800	Active TSS	K562	blood
50	chr11:71158800-71161000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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