Variant report

Variant	rs2245801
Chromosome Location	chr4:90757840-90757841
allele	A/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	REST	chr4:90757293-90759857	H1-neurons	neurons:	n/a	chr4:90758798-90758811 chr4:90758722-90758742 chr4:90758722-90758742 chr4:90757347-90757360 chr4:90758747-90758760 chr4:90758202-90758215
2	MAX	chr4:90757837-90758599	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
3	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
4	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
5	ZBTB7A	chr4:90757811-90758759	ECC-1	luminal epithelium:	n/a	chr4:90758721-90758732 chr4:90758722-90758733 chr4:90758277-90758286 chr4:90758463-90758472 chr4:90758523-90758532
6	CTCF	chr4:90757700-90757850	AG09319	gingival:	n/a	n/a
7	BACH1	chr4:90757699-90758463	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:90757760-90757910	WERI-Rb-1	eye:	n/a	n/a
9	E2F6	chr4:90757275-90758968	H1-hESC	embryonic stem cell:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521 chr4:90757373-90757383
10	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
11	MAX	chr4:90757782-90758982	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
12	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
13	ZNF263	chr4:90757349-90758919	K562	blood:	n/a	chr4:90757923-90757932
14	CTBP2	chr4:90757235-90758898	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr4:90757794-90758579	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
16	GATA1	chr4:90756797-90758328	PBDE	blood:	n/a	chr4:90758097-90758105
17	CTCF	chr4:90757760-90757910	SK-N-SH_RA	brain:	n/a	n/a
18	ZNF263	chr4:90757362-90759526	HEK293-T-REx	kidney:	n/a	chr4:90757923-90757932
19	RAD21	chr4:90757757-90759002	H1-hESC	embryonic stem cell:	n/a	chr4:90758461-90758471 chr4:90758776-90758790
20	CTCF	chr4:90757800-90757950	HMEC	breast:	n/a	n/a
21	USF2	chr4:90757827-90757840	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90757814-90757864	HCPEpiC	choroid plexus:	n/a
2	chr4:90757814-90757864	HEK293	kidney:	embryo
3	chr4:90757814-90757864	HPAEpiC	pulmonary alveolar:	n/a
4	chr4:90757814-90757864	NT2-D1	testis:	n/a
5	chr4:90757814-90757864	PANC-1	pancreas:	n/a
6	chr4:90757814-90757864	SKMC	muscle:	n/a
7	chr4:90757814-90757864	T-47D	breast:	n/a
8	chr4:90757814-90757864	AoSMC	blood vessel:	n/a
9	chr4:90757814-90757864	AG04449	skin:	fetal
10	chr4:90757814-90757864	A549	lung:	n/a
11	chr4:90757814-90757864	ECC-1	luminal epithelium:	n/a
12	chr4:90757814-90757864	AG09319	gingival:	n/a
13	chr4:90757814-90757864	Caco-2	colon:	n/a
14	chr4:90757814-90757864	SK-N-MC	brain:	n/a
15	chr4:90757814-90757864	RPTEC	kidney:	n/a
16	chr4:90757814-90757864	SK-N-SH	brain:	n/a
17	chr4:90757814-90757864	NHBE	bronchial:	n/a
18	chr4:90757814-90757864	U87	brain:	n/a
19	chr4:90757814-90757864	BE2_C	brain:	n/a
20	chr4:90757814-90757864	HCT-116	colon:	n/a
21	chr4:90757814-90757864	MCF-7	breast:	n/a
22	chr4:90757814-90757864	GM06990	blood:	n/a
23	chr4:90757814-90757864	Hela-S3	cervix:	n/a
24	chr4:90757814-90757864	ovcar-3	ovarian:	n/a
25	chr4:90757814-90757864	HCF	heart:	n/a
26	chr4:90757814-90757864	HAEpiC	amniotic membrane:	n/a
27	chr4:90757814-90757864	HCM	heart:	n/a
28	chr4:90757814-90757864	HepG2	liver:	n/a
29	chr4:90757814-90757864	AG10803	skin:	n/a
30	chr4:90757814-90757864	HNPCEpiC	eye:	n/a
31	chr4:90757814-90757864	Jurkat	blood:	n/a
32	chr4:90757814-90757864	Hepatocyte	liver:	n/a
33	chr4:90757814-90757864	K562	blood:	n/a
34	chr4:90757814-90757864	PrEC	prostate:	n/a
35	chr4:90757814-90757864	HMEC	breast:	n/a
36	chr4:90757814-90757864	SAEC	small airway:	n/a
37	chr4:90757814-90757864	IMR90	lung:	fetal
38	chr4:90757814-90757864	LNCaP	prostate:	n/a
39	chr4:90757814-90757864	AG09309	skin:	n/a
40	chr4:90757814-90757864	PFSK-1	brain:	n/a
41	chr4:90757814-90757864	HUVEC	blood vessel:	n/a
42	chr4:90757814-90757864	GM12891	blood:	n/a
43	chr4:90757814-90757864	GM12892	blood:	n/a
44	chr4:90757814-90757864	ProgFib	skin:	n/a
45	chr4:90757814-90757864	HIPEpiC	eye:	n/a
46	chr4:90757814-90757864	SK-N-SH_RA	brain:	n/a
47	chr4:90757814-90757864	NH-A	brain:	n/a
48	chr4:90757814-90757864	GM12878	blood:	n/a
49	chr4:90757814-90757864	HEEpiC	esophagus:	n/a
50	chr4:90757814-90757864	HL-60	blood:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-1	chr4:90757559-90757885	ENSG00000247775
2	lnc-MMRN1-1	chr4:90757575-90757885	ENSG00000247775
3	lnc-MMRN1-1	chr4:90757552-90757885	NONHSAT097403

Variant related genes	Relation type
SNCA	TF binding region
SNCA	CpG island

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10004413	0.80[ASN][1000 genomes]
rs10005233	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10008964	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10028246	0.94[ASN][1000 genomes]
rs12331318	0.80[ASN][1000 genomes]
rs1348224	0.96[ASN][1000 genomes]
rs1372517	0.91[ASN][1000 genomes]
rs1372518	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372519	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372520	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372521	0.94[ASN][1000 genomes]
rs1372522	0.90[ASN][1000 genomes]
rs1442144	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1442148	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1471483	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1471484	0.80[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs168550	0.85[AFR][1000 genomes]
rs1811442	0.80[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1811443	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1822217	0.94[ASN][1000 genomes]
rs1837891	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs184810	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2197120	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2301134	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2301135	1.00[ASN][1000 genomes]
rs2572318	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2572320	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2583962	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2583964	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2583968	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2583972	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2583975	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2583978	0.80[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2619341	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2619347	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2619349	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2619355	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2619356	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2619368	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2736994	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2737002	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2737010	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2737011	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2737021	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2737025	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2737028	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2737030	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28403500	0.80[ASN][1000 genomes]
rs28415623	0.91[ASN][1000 genomes]
rs28507349	0.94[ASN][1000 genomes]
rs28734152	0.80[ASN][1000 genomes]
rs28777703	0.80[ASN][1000 genomes]
rs3113355	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35424815	0.80[ASN][1000 genomes]
rs356162	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs356186	1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs356188	0.92[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs356191	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3756059	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3756063	0.91[ASN][1000 genomes]
rs3806789	0.93[ASN][1000 genomes]
rs4293762	0.91[ASN][1000 genomes]
rs58864428	0.94[ASN][1000 genomes]
rs6532191	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6532192	0.96[ASN][1000 genomes]
rs6532193	0.96[ASN][1000 genomes]
rs6816736	0.94[ASN][1000 genomes]
rs6817001	0.94[ASN][1000 genomes]
rs6828271	0.90[ASN][1000 genomes]
rs6843084	0.94[ASN][1000 genomes]
rs748849	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7672979	0.80[ASN][1000 genomes]
rs7680557	0.96[ASN][1000 genomes]
rs7680761	0.96[ASN][1000 genomes]
rs7681154	0.93[ASN][1000 genomes]
rs7681440	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7687945	0.96[ASN][1000 genomes]
rs894280	0.96[ASN][1000 genomes]
rs920624	0.94[ASN][1000 genomes]
rs990085	0.92[AMR][1000 genomes];0.91[ASN][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	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:90755800-90759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:90755800-90759600	Active TSS	Fetal Brain Female	brain
4	chr4:90756600-90758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:90756600-90758000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:90756600-90758600	Enhancers	Spleen	Spleen
7	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
8	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
9	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr4:90756800-90758000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:90756800-90758000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr4:90756800-90758200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:90756800-90758200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:90756800-90759600	Active TSS	Ovary	ovary
15	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:90757000-90758000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr4:90757000-90758000	Bivalent/Poised TSS	Fetal Kidney	kidney
18	chr4:90757000-90758200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:90757000-90758200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:90757000-90758200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:90757200-90758000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr4:90757200-90758000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:90757200-90758000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
27	chr4:90757200-90758200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:90757200-90758200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr4:90757200-90758200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
32	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
33	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
35	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:90757400-90758000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:90757400-90758000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
38	chr4:90757400-90758000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
39	chr4:90757400-90758000	Bivalent/Poised TSS	Colonic Mucosa	Colon
40	chr4:90757400-90758000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
41	chr4:90757400-90758000	Active TSS	Right Ventricle	heart
42	chr4:90757400-90758000	Flanking Active TSS	Dnd41	blood
43	chr4:90757400-90758200	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr4:90757400-90758200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr4:90757400-90758200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus

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