Variant report

Variant	rs34956990
Chromosome Location	chr4:90758508-90758509
allele	G/T
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	chr4:90758048-90759014	H1-hESC	embryonic stem cell:	n/a	n/a
2	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
3	MYC	chr4:90757889-90758516	MCF10A-Er-Src	breast:	n/a	chr4:90758080-90758090
4	CTCF	chr4:90758480-90758630	SK-N-SH_RA	brain:	n/a	n/a
5	MAX	chr4:90757886-90758637	SK-N-SH	brain:	n/a	chr4:90758080-90758090
6	POLR2A	chr4:90757941-90759580	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr4:90758000-90758525	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr4:90757982-90759110	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
9	TAF1	chr4:90758136-90758591	H1-neurons	neurons:	n/a	n/a
10	E2F6	chr4:90757956-90758737	K562	blood:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521
11	YY1	chr4:90758069-90758557	H1-hESC	embryonic stem cell:	n/a	chr4:90758461-90758475 chr4:90758401-90758415 chr4:90758458-90758469
12	MAX	chr4:90757837-90758599	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
13	POLR2A	chr4:90758021-90758573	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr4:90758068-90759085	HEK293	kidney:	n/a	n/a
15	POLR2A	chr4:90758377-90758573	K562	blood:	n/a	n/a
16	GATA2	chr4:90757246-90759504	SH-SY5Y	brain:	n/a	chr4:90758439-90758447 chr4:90758097-90758105
17	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
18	MAX	chr4:90757952-90758985	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
19	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
20	MAX	chr4:90757960-90758701	SK-N-SH	brain:	n/a	chr4:90758080-90758090
21	CTCF	chr4:90758480-90758630	AG09319	gingival:	n/a	n/a
22	POLR2A	chr4:90757959-90759244	HUVEC	blood vessel:	n/a	n/a
23	E2F4	chr4:90758400-90758600	MCF10A-Er-Src	breast:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521
24	TBP	chr4:90757998-90759047	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:90757883-90759635	H1-neurons	neurons:	n/a	n/a
26	SP4	chr4:90758220-90758688	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr4:90757892-90759167	HUVEC	blood vessel:	n/a	n/a
28	E2F6	chr4:90758379-90758621	K562	blood:	n/a	chr4:90758514-90758521 chr4:90758510-90758522 chr4:90758514-90758521 chr4:90758464-90758473 chr4:90758511-90758525 chr4:90758514-90758521
29	POLR2A	chr4:90758092-90758831	SK-N-MC	brain:	n/a	n/a
30	MYC	chr4:90758475-90759059	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB7A	chr4:90757973-90758730	ECC-1	luminal epithelium:	n/a	chr4:90758277-90758286 chr4:90758463-90758472 chr4:90758523-90758532
32	JUND	chr4:90758106-90758884	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:90757970-90759061	PBDE	blood:	n/a	n/a
34	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
35	SIN3A	chr4:90757284-90759458	H1-hESC	embryonic stem cell:	n/a	chr4:90759043-90759052
36	MAX	chr4:90757782-90758982	H1-hESC	embryonic stem cell:	n/a	chr4:90758080-90758090
37	MAX	chr4:90757869-90758613	HCT-116	colon:	n/a	chr4:90758080-90758090
38	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
39	ZNF263	chr4:90757349-90758919	K562	blood:	n/a	chr4:90757923-90757932
40	CTBP2	chr4:90757235-90758898	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr4:90757794-90758579	ECC-1	luminal epithelium:	n/a	chr4:90758080-90758090
42	MAX	chr4:90757979-90758532	K562	blood:	n/a	chr4:90758080-90758090
43	POLR2A	chr4:90757921-90759119	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAZ	chr4:90757933-90758583	IMR90	lung:	n/a	chr4:90758080-90758090
45	MAX	chr4:90757924-90758565	HCT-116	colon:	n/a	chr4:90758080-90758090
46	CTCF	chr4:90758500-90758610	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:90757983-90759083	MCF10A-Er-Src	breast:	n/a	n/a
48	SIN3AK20	chr4:90758056-90758572	H1-hESC	embryonic stem cell:	n/a	n/a
49	TAF1	chr4:90758001-90759015	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr4:90758099-90758542	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:90758469-90758519	K562	blood:	n/a
2	chr4:90758494-90758544	HEEpiC	esophagus:	n/a
3	chr4:90758494-90758544	AG10803	skin:	n/a
4	chr4:90758469-90758519	HRPEpiC	eye:	n/a
5	chr4:90758494-90758544	MCF-7	breast:	n/a
6	chr4:90758469-90758519	Hela-S3	cervix:	n/a
7	chr4:90758469-90758519	MCF-7	breast:	n/a
8	chr4:90758469-90758519	HepG2	liver:	n/a
9	chr4:90758469-90758519	HL-60	blood:	n/a
10	chr4:90758469-90758519	MCF10A-Er-Src	breast:	n/a
11	chr4:90758494-90758544	BE2_C	brain:	n/a
12	chr4:90758494-90758544	GM12892	blood:	n/a
13	chr4:90758469-90758519	HCF	heart:	n/a
14	chr4:90758494-90758544	HNPCEpiC	eye:	n/a
15	chr4:90758494-90758544	GM06990	blood:	n/a
16	chr4:90758494-90758544	AG09309	skin:	n/a
17	chr4:90758469-90758519	SKMC	muscle:	n/a
18	chr4:90758494-90758544	PrEC	prostate:	n/a
19	chr4:90758469-90758519	HIPEpiC	eye:	n/a
20	chr4:90758469-90758519	Caco-2	colon:	n/a
21	chr4:90758494-90758544	NH-A	brain:	n/a
22	chr4:90758494-90758544	GM19239	blood:	n/a
23	chr4:90758469-90758519	A549	lung:	n/a
24	chr4:90758494-90758544	HIPEpiC	eye:	n/a
25	chr4:90758494-90758544	SK-N-MC	brain:	n/a
26	chr4:90758494-90758544	LNCaP	prostate:	n/a
27	chr4:90758494-90758544	ovcar-3	ovarian:	n/a
28	chr4:90758469-90758519	Jurkat	blood:	n/a
29	chr4:90758494-90758544	PANC-1	pancreas:	n/a
30	chr4:90758469-90758519	HRCEpiC	kidney:	n/a
31	chr4:90758469-90758519	PANC-1	pancreas:	n/a
32	chr4:90758469-90758519	AG04449	skin:	fetal
33	chr4:90758494-90758544	T-47D	breast:	n/a
34	chr4:90758469-90758519	IMR90	lung:	fetal
35	chr4:90758494-90758544	HPAEpiC	pulmonary alveolar:	n/a
36	chr4:90758494-90758544	HUVEC	blood vessel:	n/a
37	chr4:90758494-90758544	BJ	skin:	n/a
38	chr4:90758494-90758544	K562	blood:	n/a
39	chr4:90758494-90758544	HRCEpiC	kidney:	n/a
40	chr4:90758469-90758519	HEK293	kidney:	embryo
41	chr4:90758469-90758519	HRE	kidney:	n/a
42	chr4:90758469-90758519	HAEpiC	amniotic membrane:	n/a
43	chr4:90758494-90758544	SAEC	small airway:	n/a
44	chr4:90758494-90758544	HCM	heart:	n/a
45	chr4:90758469-90758519	BJ	skin:	n/a
46	chr4:90758494-90758544	HL-60	blood:	n/a
47	chr4:90758469-90758519	Hepatocyte	liver:	n/a
48	chr4:90758494-90758544	HAEpiC	amniotic membrane:	n/a
49	chr4:90758469-90758519	SAEC	small airway:	n/a
50	chr4:90758469-90758519	GM12891	blood:	n/a

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs62306329	0.89[EUR][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:124 , 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	chr4:90756600-90758600	Enhancers	Spleen	Spleen
5	chr4:90756600-90759000	Active TSS	Brain Substantia Nigra	brain
6	chr4:90756600-90759400	Active TSS	Brain Anterior Caudate	brain
7	chr4:90756600-90759600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr4:90756800-90759600	Active TSS	Ovary	ovary
9	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:90757000-90759400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:90757000-90759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:90757000-90759600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr4:90757200-90758800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
15	chr4:90757200-90759400	Active TSS	Brain Hippocampus Middle	brain
16	chr4:90757200-90759600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:90757200-90759600	Active TSS	Brain Cingulate Gyrus	brain
18	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:90757400-90758600	Bivalent/Poised TSS	Psoas Muscle	Psoas
20	chr4:90757400-90758800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr4:90757400-90758800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr4:90757400-90758800	Bivalent/Poised TSS	NHDF-Ad	bronchial
23	chr4:90757400-90759000	Active TSS	HMEC	breast
24	chr4:90757400-90759400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
25	chr4:90757400-90759400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr4:90757400-90759400	Active TSS	Right Atrium	heart
27	chr4:90757400-90759600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:90757400-90759600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:90757400-90759600	Active TSS	Brain Angular Gyrus	brain
30	chr4:90757400-90759600	Active TSS	Fetal Brain Male	brain
31	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:90757600-90758600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:90757600-90758600	Active TSS	Liver	Liver
34	chr4:90757600-90758600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
35	chr4:90757600-90758800	Active TSS	Hela-S3	cervix
36	chr4:90757600-90759000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr4:90757600-90759000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
38	chr4:90757600-90759000	Active TSS	HUVEC	blood vessel
39	chr4:90757600-90759200	Bivalent/Poised TSS	Left Ventricle	heart
40	chr4:90757600-90759400	Bivalent/Poised TSS	Esophagus	oesophagus
41	chr4:90757600-90759400	Active TSS	K562	blood
42	chr4:90757600-90759600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:90757800-90758600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:90757800-90758600	Weak transcription	Fetal Heart	heart
45	chr4:90757800-90758600	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr4:90757800-90758600	Bivalent/Poised TSS	NHLF	lung
47	chr4:90757800-90758800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:90757800-90758800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:90757800-90758800	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr4:90757800-90758800	Active TSS	NH-A	brain

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