Variant report

Variant	rs3020244
Chromosome Location	chr8:6263953-6263954
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	POLR2A	chr8:6263630-6265140	H1-neurons	neurons:	n/a	n/a
2	EP300	chr8:6263843-6264186	GM12878	blood:	n/a	chr8:6264126-6264142
3	POLR2A	chr8:6263861-6264344	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr8:6263837-6264314	GM12878	blood:	n/a	chr8:6264159-6264169 chr8:6264161-6264168 chr8:6264163-6264170
5	IRF1	chr8:6263834-6264343	K562	blood:	n/a	n/a
6	POLR2A	chr8:6263820-6264356	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr8:6263787-6264410	A549	lung:	n/a	chr8:6264130-6264139 chr8:6264094-6264103
8	ZNF143	chr8:6263898-6264237	K562	blood:	n/a	n/a
9	RFX5	chr8:6263880-6264281	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr8:6263732-6264346	HCT-116	colon:	n/a	n/a
11	CREB1	chr8:6263558-6264322	A549	lung:	n/a	n/a
12	YY1	chr8:6263540-6264823	GM12892	blood:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
13	UBTF	chr8:6263123-6264244	K562	blood:	n/a	n/a
14	ZBTB7A	chr8:6263296-6264989	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr8:6263888-6264304	HepG2	liver:	n/a	n/a
16	STAT3	chr8:6263824-6264160	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr8:6263860-6264010	GM12874	blood:	n/a	n/a
18	POLR2A	chr8:6263164-6264735	GM12878	blood:	n/a	n/a
19	MXI1	chr8:6263153-6265176	HepG2	liver:	n/a	n/a
20	POLR2A	chr8:6263649-6264366	ECC-1	luminal epithelium:	n/a	n/a
21	YY1	chr8:6263438-6264539	HepG2	liver:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
22	POLR2A	chr8:6263278-6265010	NB4	blood:	n/a	n/a
23	YY1	chr8:6263806-6264562	H1-hESC	embryonic stem cell:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
24	EP300	chr8:6263800-6264269	GM12878	blood:	n/a	chr8:6264126-6264142 chr8:6264218-6264227
25	BHLHE40	chr8:6263950-6264244	GM12878	blood:	n/a	n/a
26	POLR2A	chr8:6263239-6265064	GM10847	blood:	n/a	n/a
27	RUNX3	chr8:6263785-6264338	GM12878	blood:	n/a	n/a
28	ELF1	chr8:6262891-6264569	HCT-116	colon:	n/a	n/a
29	TBL1XR1	chr8:6263932-6264219	K562	blood:	n/a	n/a
30	POLR2A	chr8:6263807-6264444	HUVEC	blood vessel:	n/a	n/a
31	YY1	chr8:6263919-6264463	SK-N-SH	brain:	n/a	chr8:6264124-6264138 chr8:6264094-6264108 chr8:6264125-6264139
32	JUND	chr8:6263320-6264317	K562	blood:	n/a	n/a
33	POLR2A	chr8:6263542-6264695	A549	lung:	n/a	n/a
34	HEY1	chr8:6263736-6264436	HepG2	liver:	n/a	n/a
35	TAF1	chr8:6263800-6264379	PFSK-1	brain:	n/a	n/a
36	SIN3AK20	chr8:6263775-6264348	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr8:6263091-6264344	HCT-116	colon:	n/a	n/a
38	CHD2	chr8:6263835-6264327	HepG2	liver:	n/a	n/a
39	E2F1	chr8:6263894-6264388	Hela-S3	cervix:	n/a	chr8:6264130-6264139 chr8:6264094-6264103
40	POLR2A	chr8:6263101-6265055	Hela-S3	cervix:	n/a	n/a
41	TCF7L2	chr8:6263837-6264190	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr8:6263837-6264346	HepG2	liver:	n/a	n/a
43	GABPA	chr8:6263769-6264563	MCF-7	breast:	n/a	chr8:6264107-6264121 chr8:6264110-6264121 chr8:6264126-6264135 chr8:6264110-6264124
44	CHD2	chr8:6263193-6264393	Hela-S3	cervix:	n/a	n/a
45	EGR1	chr8:6263948-6264322	K562	blood:	n/a	n/a
46	HA-E2F1	chr8:6263641-6264364	Hela-S3	cervix:	n/a	chr8:6264130-6264139 chr8:6264094-6264103
47	TAF1	chr8:6263617-6264520	A549	lung:	n/a	n/a
48	NFATC1	chr8:6263524-6264233	GM12878	blood:	n/a	n/a
49	POLR2A	chr8:6263662-6264563	MCF-7	breast:	n/a	n/a
50	POLR2A	chr8:6263546-6264420	GM12891	blood:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPT2-2	chr8:6263227-6264069	XLOC_006985
2	lnc-ANGPT2-2	chr8:6263227-6264069	NR_040040
3	lnc-ANGPT2-2	chr8:6262927-6264063	ENSG00000246089.3
4	lnc-ANGPT2-2	chr8:6262438-6264096	NONHSAT124771

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

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2916656	1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3020244	RP11-115C21.2	cis	Heart Left Ventricle	GTEx
rs3020244	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

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	chr8:6263000-6264000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr8:6263000-6264600	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr8:6263000-6264600	Active TSS	Aorta	Aorta
18	chr8:6263000-6264800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:6263000-6264800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr8:6263000-6264800	Active TSS	HSMMtube	muscle
21	chr8:6263000-6265000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr8:6263000-6265000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:6263000-6265000	Active TSS	Colonic Mucosa	Colon
24	chr8:6263000-6265000	Active TSS	Fetal Brain Female	brain
25	chr8:6263000-6265000	Active TSS	Fetal Intestine Large	intestine
26	chr8:6263000-6265200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr8:6263000-6265200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr8:6263000-6265200	Active TSS	Right Ventricle	heart
29	chr8:6263000-6265400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr8:6263000-6265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:6263000-6265400	Active TSS	Brain Germinal Matrix	brain
32	chr8:6263000-6265400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr8:6263000-6265600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr8:6263200-6264200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr8:6263200-6264600	Active TSS	Left Ventricle	heart
36	chr8:6263200-6264600	Active TSS	Lung	lung
37	chr8:6263200-6264600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr8:6263200-6264600	Active TSS	Spleen	Spleen
39	chr8:6263200-6264800	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr8:6263200-6264800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr8:6263200-6264800	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr8:6263200-6264800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:6263200-6264800	Active TSS	Fetal Lung	lung
44	chr8:6263200-6264800	Active TSS	Fetal Thymus	thymus
45	chr8:6263200-6264800	Active TSS	Osteobl	bone
46	chr8:6263200-6265000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:6263200-6265000	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr8:6263200-6265000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:6263200-6265000	Active TSS	Esophagus	oesophagus
50	chr8:6263200-6265000	Active TSS	Gastric	stomach

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