Variant report

Variant	rs7581764
Chromosome Location	chr2:97541238-97541239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:97541220-97541370	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr2:97541160-97541310	K562	blood:	n/a	n/a
3	CTCF	chr2:97541200-97541350	AG09319	gingival:	n/a	n/a
4	GATA2	chr2:97540935-97541539	SH-SY5Y	brain:	n/a	n/a
5	POLR2A	chr2:97539243-97541503	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:97540505-97543091	K562	blood:	n/a	n/a
7	POLR2A	chr2:97539277-97543077	K562	blood:	n/a	n/a
8	POLR2A	chr2:97537838-97552897	K562	blood:	n/a	n/a
9	POLR2A	chr2:97539500-97541285	GM12878	blood:	n/a	n/a
10	ZNF263	chr2:97541083-97542057	HEK293-T-REx	kidney:	n/a	n/a
11	POLR2A	chr2:97538088-97552551	K562	blood:	n/a	n/a
12	CTCF	chr2:97541200-97541350	Caco-2	colon:	n/a	n/a
13	POLR2A	chr2:97538469-97541757	MCF10A-Er-Src	breast:	n/a	n/a
14	MAFK	chr2:97541162-97541310	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr2:97541037-97542070	K562	blood:	n/a	n/a
16	ZMIZ1	chr2:97541003-97541533	K562	blood:	n/a	n/a
17	POLR2A	chr2:97538464-97546326	K562	blood:	n/a	n/a
18	ELK1	chr2:97541194-97541298	GM12878	blood:	n/a	n/a
19	CCNT2	chr2:97541230-97542464	K562	blood:	n/a	chr2:97542046-97542066 chr2:97541345-97541354
20	MTA3	chr2:97539280-97541275	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr2:97541112-97541629	K562	blood:	n/a	n/a
22	GATA3	chr2:97541151-97541553	SH-SY5Y	brain:	n/a	n/a
23	POLR2A	chr2:97538440-97541798	K562	blood:	n/a	n/a
24	CTCF	chr2:97541220-97541370	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
2	chr2:97540516..97542905-chr2:97593439..97596324,2	K562	blood:
3	chr2:97516134..97518414-chr2:97539957..97542072,2	K562	blood:

No data

Variant related genes	Relation type
SEMA4C	TF binding region
ENSG00000252845	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11885652	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12473528	0.85[AMR][1000 genomes]
rs13430237	0.86[MEX][hapmap]
rs2314653	0.86[MEX][hapmap]
rs4907254	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs58446419	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59271006	0.94[EUR][1000 genomes]
rs62152867	0.92[EUR][1000 genomes]
rs6750988	0.82[EUR][1000 genomes]
rs6758174	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7581764	NEURL3	cis	parietal	SCAN
rs7581764	TXNDC9	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536600-97541600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr2:97536800-97542000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:97536800-97546200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:97536800-97551800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:97537000-97542200	Enhancers	Placenta	Placenta
7	chr2:97537800-97544200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:97538000-97543800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:97538400-97541800	Enhancers	Fetal Kidney	kidney
10	chr2:97538400-97542400	Enhancers	Brain Substantia Nigra	brain
11	chr2:97538400-97544400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:97538400-97547400	Enhancers	Spleen	Spleen
13	chr2:97538600-97541800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:97538600-97542000	Enhancers	Fetal Muscle Leg	muscle
15	chr2:97538600-97542400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:97538600-97542600	Enhancers	Fetal Stomach	stomach
17	chr2:97538600-97542800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr2:97538600-97542800	Enhancers	Brain Hippocampus Middle	brain
19	chr2:97538600-97543000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:97538600-97543800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:97538600-97544800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:97538600-97545000	Enhancers	HSMMtube	muscle
23	chr2:97538800-97542400	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:97539000-97541400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:97539000-97541600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:97539000-97541600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:97539000-97541600	Weak transcription	NH-A	brain
28	chr2:97539000-97542400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:97539000-97543200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:97539200-97542400	Enhancers	Brain Anterior Caudate	brain
31	chr2:97539200-97543800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:97539400-97542400	Enhancers	Brain Angular Gyrus	brain
33	chr2:97539400-97546800	Weak transcription	Lung	lung
34	chr2:97539600-97541600	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr2:97539600-97541800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr2:97539600-97542000	Enhancers	K562	blood
37	chr2:97539600-97544600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:97539800-97542200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:97539800-97542400	Enhancers	Primary T cells from cord blood	blood
40	chr2:97539800-97542800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr2:97540000-97541400	Enhancers	Brain Germinal Matrix	brain
42	chr2:97540000-97541400	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr2:97540000-97548000	Weak transcription	Right Atrium	heart
44	chr2:97540200-97541400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:97540200-97541400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:97540200-97541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:97540200-97541400	Weak transcription	Hela-S3	cervix
48	chr2:97540200-97541600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:97540200-97541600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:97540200-97541800	Enhancers	Fetal Lung	lung

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