Variant report

Variant	rs4760597
Chromosome Location	chr12:49257602-49257603
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49255873-49258188	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:49253272-49258971	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49257591-49257641	ECC-1	luminal epithelium:	n/a
2	chr12:49257591-49257641	HMEC	breast:	n/a
3	chr12:49257591-49257641	U87	brain:	n/a
4	chr12:49257591-49257641	K562	blood:	n/a
5	chr12:49257591-49257641	PFSK-1	brain:	n/a
6	chr12:49257591-49257641	HUVEC	blood vessel:	n/a
7	chr12:49257591-49257641	A549	lung:	n/a
8	chr12:49257591-49257641	GM12878	blood:	n/a
9	chr12:49257591-49257641	CMK	blood:	n/a
10	chr12:49257591-49257641	Hela-S3	cervix:	n/a
11	chr12:49257591-49257641	SKMC	muscle:	n/a
12	chr12:49257591-49257641	NH-A	brain:	n/a
13	chr12:49257591-49257641	HNPCEpiC	eye:	n/a
14	chr12:49257591-49257641	AG04449	skin:	fetal
15	chr12:49257591-49257641	AG09319	gingival:	n/a
16	chr12:49257591-49257641	T-47D	breast:	n/a
17	chr12:49257591-49257641	GM06990	blood:	n/a
18	chr12:49257591-49257641	NB4	blood:	n/a
19	chr12:49257591-49257641	HPAEpiC	pulmonary alveolar:	n/a
20	chr12:49257591-49257641	HRE	kidney:	n/a
21	chr12:49257591-49257641	Hepatocyte	liver:	n/a
22	chr12:49257591-49257641	AG09309	skin:	n/a
23	chr12:49257591-49257641	GM19239	blood:	n/a
24	chr12:49257591-49257641	HL-60	blood:	n/a
25	chr12:49257591-49257641	HIPEpiC	eye:	n/a
26	chr12:49257591-49257641	AG10803	skin:	n/a
27	chr12:49257591-49257641	HEK293	kidney:	embryo
28	chr12:49257591-49257641	NHDF-neo	bronchial:	n/a
29	chr12:49257591-49257641	Jurkat	blood:	n/a
30	chr12:49257591-49257641	PANC-1	pancreas:	n/a
31	chr12:49257591-49257641	RPTEC	kidney:	n/a
32	chr12:49257591-49257641	HCF	heart:	n/a
33	chr12:49257591-49257641	SK-N-SH	brain:	n/a
34	chr12:49257591-49257641	NHBE	bronchial:	n/a
35	chr12:49257591-49257641	NT2-D1	testis:	n/a
36	chr12:49257591-49257641	PrEC	prostate:	n/a
37	chr12:49257591-49257641	HAEpiC	amniotic membrane:	n/a
38	chr12:49257591-49257641	LNCaP	prostate:	n/a
39	chr12:49257591-49257641	Caco-2	colon:	n/a
40	chr12:49257591-49257641	HCM	heart:	n/a
41	chr12:49257591-49257641	GM12892	blood:	n/a
42	chr12:49257591-49257641	GM12891	blood:	n/a
43	chr12:49257591-49257641	BJ	skin:	n/a
44	chr12:49257591-49257641	ProgFib	skin:	n/a
45	chr12:49257591-49257641	AoSMC	blood vessel:	n/a
46	chr12:49257591-49257641	AG04450	lung:	fetal
47	chr12:49257591-49257641	H1-hESC	embryonic stem cell:	embryo
48	chr12:49257591-49257641	SK-N-SH_RA	brain:	n/a
49	chr12:49257591-49257641	HCT-116	colon:	n/a
50	chr12:49257591-49257641	MCF-7	breast:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49253202..49256104-chr12:49256944..49260973,5	K562	blood:
2	chr12:49243430..49246231-chr12:49257385..49259059,2	K562	blood:
3	chr12:49250166..49253023-chr12:49256244..49259199,2	K562	blood:
4	chr12:49244737..49248613-chr12:49256890..49261439,8	MCF-7	breast:
5	chr12:49257214..49258853-chr12:49292105..49293671,2	MCF-7	breast:
6	chr12:49256218..49258210-chr12:49380440..49382850,2	MCF-7	breast:
7	chr12:49257454..49260772-chr12:49317154..49320539,3	MCF-7	breast:

No data

Variant related genes	Relation type
RND1	TF binding region
RND1	CpG island
ENSG00000172602	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1045340	0.89[JPT][hapmap]
rs10783285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446972	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs3759148	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782360	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760598	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760599	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760639	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4760597	RND1	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49246600-49258600	Weak transcription	Small Intestine	intestine
2	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
3	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:49247200-49258600	Weak transcription	Esophagus	oesophagus
5	chr12:49247200-49258600	Weak transcription	Right Ventricle	heart
6	chr12:49247200-49258800	Weak transcription	Right Atrium	heart
7	chr12:49247200-49259000	Weak transcription	Ovary	ovary
8	chr12:49251600-49257800	Weak transcription	Spleen	Spleen
9	chr12:49252400-49257800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:49253800-49258200	Weak transcription	HepG2	liver
11	chr12:49254800-49259000	Transcr. at gene 5' and 3'	A549	lung
12	chr12:49255400-49257800	Weak transcription	Fetal Intestine Large	intestine
13	chr12:49255400-49258000	Weak transcription	Pancreas	Pancrea
14	chr12:49255600-49257800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:49255800-49260200	Active TSS	Brain Angular Gyrus	brain
16	chr12:49256000-49258200	Flanking Active TSS	Fetal Brain Female	brain
17	chr12:49256000-49258400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49256000-49258400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:49256000-49260200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:49256200-49257800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49256200-49257800	Active TSS	Brain Hippocampus Middle	brain
22	chr12:49256200-49259000	Flanking Active TSS	Fetal Brain Male	brain
23	chr12:49256200-49259400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:49256200-49259800	Active TSS	Brain Cingulate Gyrus	brain
25	chr12:49256400-49258000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr12:49256400-49258000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:49256400-49258400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:49256400-49258800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:49256400-49260200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr12:49256600-49257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:49256600-49260000	Active TSS	Brain Anterior Caudate	brain
32	chr12:49256800-49257800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:49256800-49258000	Enhancers	Gastric	stomach
34	chr12:49256800-49258400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr12:49257000-49257800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:49257000-49258400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:49257200-49258200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr12:49257200-49259400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:49257400-49257800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr12:49257400-49257800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:49257400-49257800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:49257400-49257800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:49257400-49257800	Enhancers	GM12878-XiMat	blood
44	chr12:49257400-49258000	Enhancers	Primary B cells from cord blood	blood
45	chr12:49257400-49258200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
46	chr12:49257400-49258200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
47	chr12:49257400-49258800	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:49257400-49259000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:49257400-49259000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
50	chr12:49257400-49259000	Flanking Active TSS	Liver	Liver

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