Variant report

Variant	rs16832968
Chromosome Location	chr1:151033520-151033521
allele	C/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	REST	chr1:151031814-151033869	H1-neurons	neurons:	n/a	chr1:151032692-151032702 chr1:151032963-151032976
2	POLR2A	chr1:151033440-151033968	HUVEC	blood vessel:	n/a	n/a
3	REST	chr1:151031025-151034997	H1-neurons	neurons:	n/a	chr1:151031403-151031416 chr1:151032692-151032702 chr1:151032963-151032976
4	MAZ	chr1:151031527-151033919	K562	blood:	n/a	chr1:151033042-151033052 chr1:151032815-151032825
5	KAP1	chr1:151031845-151033830	HEK293	kidney:	n/a	n/a
6	TAF1	chr1:151033417-151033857	H1-neurons	neurons:	n/a	n/a
7	CHD1	chr1:151029888-151034886	IMR90	lung:	n/a	n/a
8	SIN3A	chr1:151030675-151033911	H1-hESC	embryonic stem cell:	n/a	chr1:151031403-151031416
9	TAF1	chr1:151033410-151033920	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:151033510-151033933	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:151030105-151033911	IMR90	lung:	n/a	n/a
12	BACH1	chr1:151033337-151033968	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr1:151033481-151033912	A549	lung:	n/a	n/a
14	REST	chr1:151033196-151033910	A549	lung:	n/a	n/a
15	POLR2A	chr1:151031419-151033794	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr1:151031597-151033898	A549	lung:	n/a	chr1:151032811-151032824
17	MAFK	chr1:151032559-151033939	K562	blood:	n/a	chr1:151033435-151033450 chr1:151033804-151033814
18	MXI1	chr1:151029883-151034838	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr1:151031585-151033971	H1-neurons	neurons:	n/a	n/a
20	MAX	chr1:151031515-151034028	A549	lung:	n/a	chr1:151033042-151033052 chr1:151032815-151032825
21	POLR2A	chr1:151033443-151034014	SK-N-SH	brain:	n/a	n/a
22	EP300	chr1:151029972-151034687	SK-N-SH	brain:	n/a	chr1:151031911-151031920 chr1:151031778-151031794 chr1:151031908-151031924 chr1:151030872-151030881 chr1:151030649-151030663 chr1:151033804-151033811 chr1:151031736-151031750 chr1:151030871-151030885 chr1:151030308-151030322
23	POLR2A	chr1:151033434-151034035	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr1:151031501-151034126	SK-N-SH	brain:	n/a	chr1:151032811-151032824
25	POLR2A	chr1:151031693-151033962	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
2	chr1:151032665..151034303-chr1:151119415..151121131,2	MCF-7	breast:
3	chr1:150946136..150947648-chr1:151031480..151034167,2	MCF-7	breast:
4	chr1:151032358..151034155-chr1:151161962..151163858,2	MCF-7	breast:
5	chr1:151032560..151034898-chr1:151112557..151115397,2	MCF-7	breast:
6	chr1:151030654..151033886-chr1:151224560..151228363,4	MCF-7	breast:
7	chr1:150979106..150980954-chr1:151030690..151033653,4	K562	blood:
8	chr1:151032375..151034566-chr1:151127124..151130341,3	K562	blood:
9	chr1:150946206..150948952-chr1:151031959..151033620,2	K562	blood:
10	chr1:150550257..150553118-chr1:151032954..151034496,2	K562	blood:
11	chr1:150979291..150984938-chr1:151030285..151033653,10	K562	blood:
12	chr1:150941235..150942777-chr1:151033520..151036344,2	K562	blood:
13	chr1:150967045..150969733-chr1:151032331..151034733,2	K562	blood:
14	chr1:151032215..151035377-chr20:48807213..48809551,3	MCF-7	breast:
15	chr1:150945380..150948952-chr1:151032100..151034454,3	K562	blood:
16	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
17	chr1:150996357..150999455-chr1:151032530..151036839,3	K562	blood:
18	chr1:151029301..151033715-chr1:151136820..151141213,5	MCF-7	breast:

Variant related genes	Relation type
CDC42SE1	TF binding region
ENSG00000163141	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11800088	1.00[AMR][1000 genomes]
rs11800715	1.00[AMR][1000 genomes]
rs11804061	1.00[AMR][1000 genomes]
rs11804474	1.00[AMR][1000 genomes]
rs11806302	1.00[AMR][1000 genomes]
rs11809569	1.00[AMR][1000 genomes]
rs11809979	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs11811310	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs16832965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832988	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833008	1.00[AMR][1000 genomes]
rs16833052	0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs16833054	1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs16833100	1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs16833109	1.00[AMR][1000 genomes]
rs34570433	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41445244	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657146	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151030200-151035600	Active TSS	HSMMtube	muscle
2	chr1:151030400-151034200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151030400-151034400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:151030600-151034800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151030600-151035200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:151030800-151033600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:151030800-151033800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151030800-151033800	Active TSS	Right Atrium	heart
9	chr1:151030800-151034000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:151030800-151034000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:151030800-151034200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:151030800-151034200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:151030800-151034400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:151030800-151034400	Active TSS	NHLF	lung
15	chr1:151030800-151034600	Active TSS	Thymus	Thymus
16	chr1:151030800-151034800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:151030800-151035200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:151030800-151035400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:151030800-151035800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:151031000-151033600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr1:151031000-151033600	Active TSS	NHDF-Ad	bronchial
22	chr1:151031000-151033800	Active TSS	Right Ventricle	heart
23	chr1:151031000-151034000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:151031000-151034000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:151031000-151034400	Active TSS	HSMM	muscle
26	chr1:151031000-151034600	Active TSS	Brain Anterior Caudate	brain
27	chr1:151031000-151034600	Active TSS	A549	lung
28	chr1:151031000-151035200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:151031200-151034000	Active TSS	Fetal Intestine Small	intestine
30	chr1:151031200-151034200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr1:151031200-151034600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:151031200-151034800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:151031200-151035800	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:151031400-151033600	Active TSS	Placenta Amnion	Placenta Amnion
35	chr1:151031400-151033800	Active TSS	Left Ventricle	heart
36	chr1:151031400-151033800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:151031400-151034200	Active TSS	Fetal Intestine Large	intestine
38	chr1:151031400-151034200	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:151031400-151034800	Active TSS	Fetal Brain Male	brain
40	chr1:151031400-151035600	Active TSS	Brain Angular Gyrus	brain
41	chr1:151031400-151035800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:151031600-151033600	Active TSS	Stomach Smooth Muscle	stomach
43	chr1:151031600-151034200	Active TSS	Dnd41	blood
44	chr1:151031600-151035200	Active TSS	Fetal Brain Female	brain
45	chr1:151031600-151035600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:151031600-151035600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:151031800-151034600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:151031800-151035200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:151032000-151033600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:151032200-151033600	Flanking Active TSS	Primary B cells from cord blood	blood

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