Variant report

Variant	rs4601596
Chromosome Location	chr1:221914458-221914459
allele	C/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	chr1:221914026-221914903	GM12891	blood:	n/a	n/a
2	RAD21	chr1:221913441-221917304	IMR90	lung:	n/a	chr1:221916643-221916657 chr1:221915692-221915706
3	SIN3A	chr1:221913975-221914540	GM12878	blood:	n/a	chr1:221914188-221914196
4	POLR2A	chr1:221913461-221917502	GM18526	blood:	n/a	n/a
5	JUND	chr1:221913430-221916491	SK-N-SH	brain:	n/a	chr1:221915656-221915665 chr1:221916021-221916035 chr1:221916217-221916226 chr1:221915505-221915514 chr1:221916221-221916230 chr1:221914973-221914982
6	POLR2A	chr1:221913364-221917603	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:221913521-221916519	K562	blood:	n/a	n/a
8	CHD1	chr1:221914149-221917620	GM12878	blood:	n/a	chr1:221916212-221916222
9	RFX5	chr1:221913575-221917269	SK-N-SH	brain:	n/a	chr1:221915670-221915679 chr1:221917085-221917094
10	POLR2A	chr1:221914302-221914524	GM12878	blood:	n/a	n/a
11	CHD2	chr1:221914185-221914596	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:221914185-221916766	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr1:221914411-221914480	MCF-7	breast:	n/a	n/a
14	CTCF	chr1:221914420-221914570	AG04449	skin:	n/a	n/a
15	POLR2A	chr1:221909168-221918546	GM12878	blood:	n/a	n/a
16	BHLHE40	chr1:221914316-221914497	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:221914307-221916265	H1-neurons	neurons:	n/a	n/a
18	MTA3	chr1:221913418-221914606	GM12878	blood:	n/a	n/a
19	CHD2	chr1:221914453-221914718	K562	blood:	n/a	n/a
20	MAX	chr1:221914084-221914813	GM12878	blood:	n/a	n/a
21	REST	chr1:221913953-221916571	H1-neurons	neurons:	n/a	chr1:221915151-221915171 chr1:221915151-221915171 chr1:221915155-221915168 chr1:221914189-221914197
22	CTCF	chr1:221914320-221914470	HCPEpiC	choroid plexus:	n/a	n/a
23	RCOR1	chr1:221914274-221914538	K562	blood:	n/a	n/a
24	MYC	chr1:221914100-221916901	NB4	blood:	n/a	chr1:221916101-221916110 chr1:221916100-221916110
25	POLR2A	chr1:221909243-221918347	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:221913221-221917867	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:221913969-221915911	HepG2	liver:	n/a	n/a
28	BRCA1	chr1:221914397-221914495	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:221914070-221914854	GM12878	blood:	n/a	n/a
30	MXI1	chr1:221914295-221916937	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:221913746-221918072	GM18505	blood:	n/a	n/a
32	SMC3	chr1:221914031-221914530	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:221913855-221914664	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:221913322-221917588	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:221913773-221916966	HL-60	blood:	n/a	n/a
36	BHLHE40	chr1:221913577-221914613	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:221909298-221917710	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:221914106-221914976	GM12892	blood:	n/a	n/a
39	CUX1	chr1:221914324-221914552	K562	blood:	n/a	n/a
40	NRF1	chr1:221914311-221914616	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:221905289-221917384	K562	blood:	n/a	n/a
42	POLR2A	chr1:221914095-221914903	GM12891	blood:	n/a	n/a
43	TAF1	chr1:221914348-221915935	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr1:221913884-221917487	GM18951	blood:	n/a	n/a
45	MXI1	chr1:221914047-221917430	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr1:221914205-221914553	K562	blood:	n/a	n/a
47	POLR2A	chr1:221913392-221917733	IMR90	lung:	n/a	n/a
48	MXI1	chr1:221913610-221917439	SK-N-SH	brain:	n/a	n/a
49	MAZ	chr1:221913623-221917097	IMR90	lung:	n/a	chr1:221916895-221916904 chr1:221916101-221916110 chr1:221916100-221916110 chr1:221913924-221913934
50	POLR2A	chr1:221914322-221917335	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:221912612..221914842-chr1:222041850..222044308,2	MCF-7	breast:
2	chr1:221882652..221891989-chr1:221912814..221917285,15	K562	blood:
3	chr1:221900620..221902911-chr1:221912175..221914927,2	MCF-7	breast:
4	chr1:221828900..221831688-chr1:221913117..221915245,2	K562	blood:

Variant related genes	Relation type
DUSP10	TF binding region
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10218652	0.84[EUR][1000 genomes]
rs10779456	0.91[CEU][hapmap]
rs10863653	0.82[EUR][1000 genomes]
rs10863654	0.84[EUR][1000 genomes]
rs10863655	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10863656	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11118844	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118847	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118854	0.82[EUR][1000 genomes]
rs11118857	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11118859	0.82[EUR][1000 genomes]
rs11118860	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12070192	0.84[EUR][1000 genomes]
rs12136350	0.81[EUR][1000 genomes]
rs12144586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403995	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17010720	0.84[EUR][1000 genomes]
rs4433402	0.84[EUR][1000 genomes]
rs4589119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623704	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs58850477	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6604669	0.84[JPT][hapmap]
rs66522549	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6655994	0.91[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7516292	0.82[EUR][1000 genomes]
rs7518806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221911400-221916800	Active TSS	Brain Anterior Caudate	brain
2	chr1:221911600-221917200	Active TSS	Brain Angular Gyrus	brain
3	chr1:221911800-221916800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr1:221912200-221916800	Active TSS	Colon Smooth Muscle	Colon
5	chr1:221912400-221914600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:221912400-221916800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:221912800-221917000	Active TSS	Brain Hippocampus Middle	brain
8	chr1:221912800-221917000	Active TSS	Brain Substantia Nigra	brain
9	chr1:221912800-221917200	Active TSS	HSMMtube	muscle
10	chr1:221913000-221914800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:221913000-221916600	Active TSS	Fetal Muscle Trunk	muscle
12	chr1:221913000-221917400	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:221913200-221914600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:221913200-221915000	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr1:221913200-221916000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:221913200-221916800	Active TSS	Fetal Brain Female	brain
17	chr1:221913200-221917000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:221913200-221917000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:221913200-221917000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:221913200-221917000	Active TSS	NHLF	lung
21	chr1:221913200-221917400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:221913400-221914600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:221913400-221914600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:221913400-221914600	Flanking Active TSS	Dnd41	blood
25	chr1:221913400-221915000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:221913400-221915000	Flanking Active TSS	Fetal Thymus	thymus
27	chr1:221913400-221917000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:221913400-221917000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:221913400-221917000	Active TSS	NHDF-Ad	bronchial
30	chr1:221913400-221917400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:221913600-221914600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:221913600-221914600	Flanking Active TSS	Fetal Lung	lung
33	chr1:221913600-221914600	Flanking Active TSS	Right Ventricle	heart
34	chr1:221913600-221914600	Flanking Active TSS	NHEK	skin
35	chr1:221913600-221914800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:221913600-221914800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:221913600-221914800	Flanking Active TSS	K562	blood
38	chr1:221913600-221915000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:221913600-221915000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:221913600-221915000	Flanking Active TSS	Hela-S3	cervix
41	chr1:221913600-221916600	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:221913600-221916800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:221913600-221916800	Active TSS	Liver	Liver
44	chr1:221913600-221916800	Active TSS	HMEC	breast
45	chr1:221913600-221916800	Active TSS	NH-A	brain
46	chr1:221913600-221917000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:221913600-221917000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:221913600-221917000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:221913600-221917000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
50	chr1:221913600-221917200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links