Variant report

Variant	rs1656379
Chromosome Location	chr3:158288773-158288774
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	MAX	chr3:158288657-158290566	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr3:158288556-158289240	A549	lung:	n/a	chr3:158288882-158288893 chr3:158288883-158288892 chr3:158288915-158288936
3	POLR2A	chr3:158288582-158289392	SK-N-MC	brain:	n/a	n/a
4	E2F6	chr3:158288700-158289608	K562	blood:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
5	E2F6	chr3:158288579-158289569	A549	lung:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
6	MAX	chr3:158288584-158289753	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr3:158288651-158289182	H1-hESC	embryonic stem cell:	n/a	chr3:158288897-158288910
8	ELF1	chr3:158288763-158289054	K562	blood:	n/a	chr3:158288958-158288970
9	E2F4	chr3:158288722-158289216	MCF10A-Er-Src	breast:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
10	POLR2A	chr3:158288736-158289227	U87	brain:	n/a	n/a
11	SIN3AK20	chr3:158288705-158289205	PANC-1	pancreas:	n/a	n/a
12	FOXA2	chr3:158288707-158289167	A549	lung:	n/a	n/a
13	EP300	chr3:158288676-158289149	K562	blood:	n/a	chr3:158288958-158288974
14	CHD2	chr3:158288645-158289280	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:158288715-158289298	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr3:158288702-158289568	A549	lung:	n/a	n/a
17	ZNF384	chr3:158288697-158289169	K562	blood:	n/a	n/a
18	SIN3A	chr3:158288602-158289202	H1-hESC	embryonic stem cell:	n/a	chr3:158288862-158288875
19	POLR2A	chr3:158288559-158289331	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr3:158288657-158289366	Gliobla	brain:	n/a	n/a
21	RFX5	chr3:158288713-158289096	K562	blood:	n/a	chr3:158288858-158288873 chr3:158288855-158288870 chr3:158288859-158288868 chr3:158288856-158288870 chr3:158288858-158288873 chr3:158288858-158288873
22	USF1	chr3:158288722-158289288	A549	lung:	n/a	n/a
23	E2F6	chr3:158288503-158289660	H1-hESC	embryonic stem cell:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
24	TAF1	chr3:158288674-158289258	H1-neurons	neurons:	n/a	n/a
25	E2F6	chr3:158288648-158290616	H1-hESC	embryonic stem cell:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
26	POLR2A	chr3:158288659-158289179	ECC-1	luminal epithelium:	n/a	n/a
27	SP1	chr3:158288719-158289012	H1-hESC	embryonic stem cell:	n/a	chr3:158288882-158288893 chr3:158288883-158288892 chr3:158288915-158288936
28	CEBPB	chr3:158288740-158289047	K562	blood:	n/a	n/a
29	CREB1	chr3:158288607-158289288	K562	blood:	n/a	chr3:158288897-158288910
30	USF1	chr3:158288634-158289226	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr3:158288755-158289164	A549	lung:	n/a	n/a
32	USF1	chr3:158288769-158289109	A549	lung:	n/a	n/a
33	USF1	chr3:158288682-158289169	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:158288657-158289723	MCF-7	breast:	n/a	n/a
35	CBX3	chr3:158288743-158289150	K562	blood:	n/a	n/a
36	PML	chr3:158288680-158289356	K562	blood:	n/a	n/a
37	RCOR1	chr3:158288536-158289405	K562	blood:	n/a	n/a
38	TBP	chr3:158288672-158289278	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr3:158288572-158289630	MCF-7	breast:	n/a	n/a
40	ZMIZ1	chr3:158288713-158289157	K562	blood:	n/a	n/a
41	ZC3H11A	chr3:158288451-158289222	K562	blood:	n/a	n/a
42	WRNIP1	chr3:158288724-158289137	GM12878	blood:	n/a	n/a
43	CREB1	chr3:158288708-158289020	A549	lung:	n/a	chr3:158288897-158288910
44	POLR2A	chr3:158288591-158289389	H1-hESC	embryonic stem cell:	n/a	n/a
45	CEBPB	chr3:158288697-158289043	H1-hESC	embryonic stem cell:	n/a	n/a
46	GATA3	chr3:158288763-158289213	T-47D	breast:	n/a	n/a
47	MYC	chr3:158288724-158289551	K562	blood:	n/a	n/a
48	NR2F2	chr3:158288450-158289482	K562	blood:	n/a	n/a
49	NRF1	chr3:158288663-158289053	K562	blood:	n/a	n/a
50	TBP	chr3:158288447-158289362	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158284750..158291147-chr3:158359832..158364955,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LXN-1	chr3:158287960-158288855	ENSG00000243150
2	lnc-LXN-1	chr3:158288558-158288858	NONHSAT092927
3	lnc-MLF1-1	chr3:158288770-158289024	l_2517_chr3:158282276-158289024_testes

Variant related genes	Relation type
MLF1	TF binding region
ENSG00000243150	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1369561	1.00[LWK][hapmap]
rs1435644	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1656378	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714505	1.00[LWK][hapmap]
rs1714515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1946556	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2099484	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2566339	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2566341	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2566343	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2573182	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2639656	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731114	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731116	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2731119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2731121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2915059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1013242	chr3:158275578-158305894	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013112	chr3:158280085-158301728	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1001944	chr3:158280085-158305210	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999408	chr3:158280085-158316431	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3327979	chr3:158288708-158291006	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1656379	RARRES1	cis	parietal	SCAN
rs1656379	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs1656379	TRIM59	cis	cerebellum	SCAN
rs1656379	B3GALNT1	cis	cerebellum	SCAN
rs1656379	LXN	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158288200-158288800	Flanking Active TSS	Brain Anterior Caudate	brain
2	chr3:158288200-158288800	Flanking Active TSS	Colon Smooth Muscle	Colon
3	chr3:158288200-158288800	Flanking Active TSS	NHDF-Ad	bronchial
4	chr3:158288200-158289400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr3:158288200-158289600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:158288200-158290000	Active TSS	Brain Substantia Nigra	brain
7	chr3:158288200-158290200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:158288200-158290600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:158288400-158288800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:158288400-158288800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:158288400-158288800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr3:158288400-158288800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:158288400-158288800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
14	chr3:158288400-158288800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr3:158288400-158288800	Flanking Active TSS	Fetal Heart	heart
16	chr3:158288400-158288800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
17	chr3:158288400-158288800	Flanking Active TSS	Fetal Lung	lung
18	chr3:158288400-158288800	Flanking Active TSS	Fetal Muscle Leg	muscle
19	chr3:158288400-158288800	Flanking Active TSS	Fetal Stomach	stomach
20	chr3:158288400-158288800	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr3:158288400-158288800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:158288400-158288800	Flanking Active TSS	A549	lung
23	chr3:158288400-158288800	Flanking Active TSS	Osteobl	bone
24	chr3:158288400-158289000	Active TSS	Duodenum Mucosa	Duodenum
25	chr3:158288400-158289200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:158288400-158289200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:158288400-158289200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:158288400-158289200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr3:158288400-158289200	ZNF genes & repeats	Fetal Brain Male	brain
30	chr3:158288400-158289200	Active TSS	Ovary	ovary
31	chr3:158288400-158289400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:158288400-158289400	Active TSS	Aorta	Aorta
33	chr3:158288400-158289400	Flanking Active TSS	NH-A	brain
34	chr3:158288400-158289600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:158288400-158289600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr3:158288400-158289600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:158288400-158289600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr3:158288400-158289600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr3:158288400-158289600	Active TSS	Psoas Muscle	Psoas
40	chr3:158288400-158289800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:158288400-158290000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:158288400-158290000	Active TSS	Brain Germinal Matrix	brain
43	chr3:158288400-158290000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:158288400-158290200	Active TSS	Right Ventricle	heart
45	chr3:158288400-158290400	Active TSS	Fetal Kidney	kidney
46	chr3:158288400-158292000	Active TSS	Right Atrium	heart
47	chr3:158288600-158288800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
48	chr3:158288600-158288800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr3:158288600-158288800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:158288600-158288800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links