Variant report

Variant	rs2305023
Chromosome Location	chr8:6264130-6264131
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	CTCF	chr8:6264100-6264250	HBMEC	blood vessel:	n/a	n/a
2	POLR2A	chr8:6263630-6265140	H1-neurons	neurons:	n/a	n/a
3	EP300	chr8:6263843-6264186	GM12878	blood:	n/a	chr8:6264126-6264142
4	POLR2A	chr8:6263861-6264344	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr8:6263837-6264314	GM12878	blood:	n/a	chr8:6264159-6264169 chr8:6264161-6264168 chr8:6264163-6264170
6	IRF1	chr8:6263834-6264343	K562	blood:	n/a	n/a
7	POLR2A	chr8:6263820-6264356	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr8:6263787-6264410	A549	lung:	n/a	chr8:6264130-6264139 chr8:6264094-6264103
9	ZNF143	chr8:6263898-6264237	K562	blood:	n/a	n/a
10	RFX5	chr8:6263880-6264281	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr8:6263732-6264346	HCT-116	colon:	n/a	n/a
12	CREB1	chr8:6263558-6264322	A549	lung:	n/a	n/a
13	SIX5	chr8:6263978-6264231	A549	lung:	n/a	n/a
14	YY1	chr8:6263540-6264823	GM12892	blood:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
15	UBTF	chr8:6263123-6264244	K562	blood:	n/a	n/a
16	ZBTB7A	chr8:6263296-6264989	ECC-1	luminal epithelium:	n/a	n/a
17	RCOR1	chr8:6263888-6264304	HepG2	liver:	n/a	n/a
18	STAT3	chr8:6263824-6264160	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr8:6263164-6264735	GM12878	blood:	n/a	n/a
20	MXI1	chr8:6263153-6265176	HepG2	liver:	n/a	n/a
21	POLR2A	chr8:6263649-6264366	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr8:6263438-6264539	HepG2	liver:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
23	MAFK	chr8:6263992-6264195	HepG2	liver:	n/a	n/a
24	POLR2A	chr8:6263278-6265010	NB4	blood:	n/a	n/a
25	YY1	chr8:6263806-6264562	H1-hESC	embryonic stem cell:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
26	USF1	chr8:6263975-6264344	SK-N-SH	brain:	n/a	n/a
27	YY1	chr8:6264075-6264258	K562	blood:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
28	MYC	chr8:6264048-6264243	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr8:6264060-6264210	HUVEC	blood vessel:	n/a	n/a
30	EP300	chr8:6263800-6264269	GM12878	blood:	n/a	chr8:6264126-6264142 chr8:6264218-6264227
31	GABPA	chr8:6263970-6264304	HepG2	liver:	n/a	chr8:6264107-6264121 chr8:6264110-6264121 chr8:6264126-6264135 chr8:6264110-6264124
32	GABPA	chr8:6263984-6264305	HepG2	liver:	n/a	chr8:6264107-6264121 chr8:6264110-6264121 chr8:6264126-6264135 chr8:6264110-6264124
33	FOS	chr8:6264041-6264189	MCF10A-Er-Src	breast:	n/a	n/a
34	BHLHE40	chr8:6263950-6264244	GM12878	blood:	n/a	n/a
35	POLR2A	chr8:6263239-6265064	GM10847	blood:	n/a	n/a
36	RUNX3	chr8:6263785-6264338	GM12878	blood:	n/a	n/a
37	ELF1	chr8:6262891-6264569	HCT-116	colon:	n/a	n/a
38	TBL1XR1	chr8:6263932-6264219	K562	blood:	n/a	n/a
39	PBX3	chr8:6264071-6264227	GM12878	blood:	n/a	n/a
40	POLR2A	chr8:6263807-6264444	HUVEC	blood vessel:	n/a	n/a
41	YY1	chr8:6263919-6264463	SK-N-SH	brain:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
42	JUND	chr8:6263320-6264317	K562	blood:	n/a	n/a
43	ZBTB33	chr8:6264042-6264273	A549	lung:	n/a	n/a
44	POLR2A	chr8:6263542-6264695	A549	lung:	n/a	n/a
45	HEY1	chr8:6263736-6264436	HepG2	liver:	n/a	n/a
46	TAF1	chr8:6263800-6264379	PFSK-1	brain:	n/a	n/a
47	SIN3AK20	chr8:6263775-6264348	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr8:6263091-6264344	HCT-116	colon:	n/a	n/a
49	CHD2	chr8:6263835-6264327	HepG2	liver:	n/a	n/a
50	E2F1	chr8:6263894-6264388	Hela-S3	cervix:	n/a	chr8:6264130-6264139 chr8:6264094-6264103

No.	Distal block	Cell Line	Cell type
1	chr8:6262974..6265715-chr8:6564962..6567789,4	MCF-7	breast:
2	chr17:49196178..49198302-chr8:6264048..6265705,2	K562	blood:
3	chr8:6263561..6264353-chrX:135962392..135963076,2	NB4	blood:
4	chr8:6262444..6265412-chr8:6565205..6567179,2	K562	blood:
5	chr8:6263912..6265972-chr8:6565205..6568456,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPT2-2	chr8:6264049-6264229	ENSG00000246089

Variant related genes	Relation type
MCPH1	TF binding region
ENSG00000246089	TF binding region
ENSG00000008294	Chromatin interaction
ENSG00000249898	Chromatin interaction
ENSG00000147274	Chromatin interaction
ENSG00000155189	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10104006	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10104726	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10110173	0.85[ASN][1000 genomes]
rs10110198	0.85[ASN][1000 genomes]
rs1057187	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1073908	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11137017	0.85[ASN][1000 genomes]
rs11137018	0.85[ASN][1000 genomes]
rs11137020	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11137023	0.91[ASN][1000 genomes]
rs11774902	0.90[ASN][1000 genomes]
rs11784404	0.86[ASN][1000 genomes]
rs12155753	0.84[ASN][1000 genomes]
rs12155990	0.83[ASN][1000 genomes]
rs13261141	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13268147	0.85[ASN][1000 genomes]
rs13276193	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13276518	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13276811	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1550688	0.90[ASN][1000 genomes]
rs1596457	0.85[ASN][1000 genomes]
rs1992590	0.85[ASN][1000 genomes]
rs2243661	0.84[ASN][1000 genomes]
rs2243662	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243675	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243755	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243756	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408287	0.85[ASN][1000 genomes]
rs2440453	0.94[ASN][1000 genomes]
rs2515485	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2897894	0.85[ASN][1000 genomes]
rs4601338	0.85[ASN][1000 genomes]
rs4840959	0.85[ASN][1000 genomes]
rs6559159	0.85[ASN][1000 genomes]
rs6981233	0.82[ASN][1000 genomes]
rs7018255	0.85[ASN][1000 genomes]
rs725438	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1018782	chr8:5984032-6284373	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
4	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv949501	chr8:6081704-6303511	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer 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	7 gene(s)	inside rSNPs	diseases
6	nsv890041	chr8:6084048-6274963	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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	7 gene(s)	inside rSNPs	diseases
7	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1024103	chr8:6124125-6303511	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1026950	chr8:6127991-6303511	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1025734	chr8:6128828-6303511	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1022940	chr8:6128828-6304814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv527005	chr8:6129051-6287170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1028552	chr8:6129221-6303511	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1021800	chr8:6144798-6286635	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1026004	chr8:6144798-6307692	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv539431	chr8:6144798-6307692	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS 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	6 gene(s)	inside rSNPs	diseases
18	nsv933107	chr8:6173244-6312807	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1018882	chr8:6204857-6289937	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv531468	chr8:6248682-6309194	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1033935	chr8:6262180-6275753	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv524404	chr8:6263083-6291485	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2305023	MCPH1	Cis_1M	lymphoblastoid	RTeQTL
rs2305023	RP11-115C21.2	cis	Adipose Subcutaneous	GTEx
rs2305023	RP11-115C21.2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6262000-6265200	Active TSS	GM12878-XiMat	blood
2	chr8:6262200-6265400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr8:6262600-6265200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr8:6262800-6264600	Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr8:6262800-6264800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr8:6262800-6264800	Active TSS	Brain Angular Gyrus	brain
7	chr8:6262800-6264800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr8:6262800-6265000	Active TSS	NHLF	lung
9	chr8:6262800-6265200	Active TSS	Brain Anterior Caudate	brain
10	chr8:6262800-6265200	Active TSS	Fetal Kidney	kidney
11	chr8:6262800-6265400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr8:6262800-6265400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr8:6262800-6265400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:6262800-6265600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:6263000-6264600	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr8:6263000-6264600	Active TSS	Aorta	Aorta
17	chr8:6263000-6264800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:6263000-6264800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr8:6263000-6264800	Active TSS	HSMMtube	muscle
20	chr8:6263000-6265000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr8:6263000-6265000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr8:6263000-6265000	Active TSS	Colonic Mucosa	Colon
23	chr8:6263000-6265000	Active TSS	Fetal Brain Female	brain
24	chr8:6263000-6265000	Active TSS	Fetal Intestine Large	intestine
25	chr8:6263000-6265200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr8:6263000-6265200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr8:6263000-6265200	Active TSS	Right Ventricle	heart
28	chr8:6263000-6265400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr8:6263000-6265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr8:6263000-6265400	Active TSS	Brain Germinal Matrix	brain
31	chr8:6263000-6265400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr8:6263000-6265600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr8:6263200-6264200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr8:6263200-6264600	Active TSS	Left Ventricle	heart
35	chr8:6263200-6264600	Active TSS	Lung	lung
36	chr8:6263200-6264600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr8:6263200-6264600	Active TSS	Spleen	Spleen
38	chr8:6263200-6264800	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr8:6263200-6264800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:6263200-6264800	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr8:6263200-6264800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr8:6263200-6264800	Active TSS	Fetal Lung	lung
43	chr8:6263200-6264800	Active TSS	Fetal Thymus	thymus
44	chr8:6263200-6264800	Active TSS	Osteobl	bone
45	chr8:6263200-6265000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:6263200-6265000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr8:6263200-6265000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr8:6263200-6265000	Active TSS	Esophagus	oesophagus
49	chr8:6263200-6265000	Active TSS	Gastric	stomach
50	chr8:6263200-6265000	Active TSS	Ovary	ovary

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