Variant report

Variant	rs422309
Chromosome Location	chr5:9544396-9544397
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	FOXM1	chr5:9544362-9544947	GM12878	blood:	n/a	n/a
2	RAD21	chr5:9544392-9545164	MCF-7	breast:	n/a	chr5:9544752-9544771 chr5:9544754-9544766 chr5:9544756-9544766
3	RAD21	chr5:9544383-9544966	SK-N-SH_RA	brain:	n/a	chr5:9544752-9544771 chr5:9544754-9544766 chr5:9544756-9544766
4	POLR2A	chr5:9544341-9545082	GM12892	blood:	n/a	n/a
5	SMC3	chr5:9544371-9545177	GM12878	blood:	n/a	chr5:9544604-9544611 chr5:9544756-9544770 chr5:9544756-9544766
6	BHLHE40	chr5:9544301-9544931	GM12878	blood:	n/a	chr5:9544752-9544768 chr5:9544912-9544928
7	CTCF	chr5:9544260-9544410	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr5:9544314-9545180	A549	lung:	n/a	chr5:9544755-9544771 chr5:9544756-9544769 chr5:9544756-9544769 chr5:9544754-9544772
9	CTCF	chr5:9544360-9544510	GM12868	blood:	n/a	n/a
10	CTCF	chr5:9544386-9545084	MCF-7	breast:	n/a	chr5:9544755-9544771 chr5:9544756-9544769 chr5:9544756-9544769 chr5:9544754-9544772
11	POLR2A	chr5:9544189-9548175	IMR90	lung:	n/a	n/a
12	CTCF	chr5:9544354-9545116	GM12878	blood:	n/a	chr5:9544755-9544771 chr5:9544756-9544769 chr5:9544756-9544769 chr5:9544754-9544772
13	RAD21	chr5:9543314-9545824	SK-N-SH	brain:	n/a	chr5:9545787-9545801 chr5:9544752-9544771 chr5:9544754-9544766 chr5:9545801-9545811 chr5:9544756-9544766 chr5:9545295-9545305
14	EGR1	chr5:9544236-9545001	MCF-7	breast:	n/a	chr5:9544690-9544705 chr5:9544688-9544702 chr5:9544627-9544637 chr5:9544691-9544704 chr5:9544691-9544704 chr5:9544690-9544704
15	CTCF	chr5:9544177-9545286	SK-N-SH	brain:	n/a	chr5:9544755-9544771 chr5:9544756-9544769 chr5:9544756-9544769 chr5:9544754-9544772
16	SMC3	chr5:9544115-9546265	SK-N-SH	brain:	n/a	chr5:9544604-9544611 chr5:9544756-9544770 chr5:9544756-9544766 chr5:9545328-9545338 chr5:9545801-9545811
17	RAD21	chr5:9544261-9547090	IMR90	lung:	n/a	chr5:9545787-9545801 chr5:9544752-9544771 chr5:9544754-9544766 chr5:9545801-9545811 chr5:9544756-9544766 chr5:9545295-9545305
18	MAZ	chr5:9544024-9548426	IMR90	lung:	n/a	chr5:9547821-9547831 chr5:9545804-9545814 chr5:9547149-9547159 chr5:9545538-9545548

No.	Distal block	Cell Line	Cell type
1	chr5:7896681..7897358-chr5:9544262..9544852,2	K562	blood:
2	chr5:9543479..9545232-chr5:9559885..9561800,2	MCF-7	breast:
3	chr5:9516858..9517435-chr5:9544318..9545210,4	MCF-7	breast:
4	chr5:9361616..9362826-chr5:9543590..9545181,8	MCF-7	breast:
5	chr5:9516481..9517369-chr5:9544330..9545219,4	MCF-7	breast:

Variant related genes	Relation type
SNHG18	TF binding region
SNORD123	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10462868	0.88[ASN][1000 genomes]
rs10475468	0.91[AFR][1000 genomes]
rs11749803	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11958932	0.82[AFR][1000 genomes]
rs1334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1398337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1508798	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1614229	0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1651283	1.00[JPT][hapmap]
rs1651284	1.00[JPT][hapmap]
rs1651285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1651286	0.88[ASN][1000 genomes]
rs1706987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1706992	0.85[ASN][1000 genomes]
rs268555	1.00[ASN][1000 genomes]
rs268556	1.00[ASN][1000 genomes]
rs374218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777371	0.82[AFR][1000 genomes]
rs3798090	0.82[AFR][1000 genomes]
rs3798092	0.91[AFR][1000 genomes]
rs3798099	1.00[ASN][1000 genomes]
rs414396	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs414829	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs431288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs432989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs456885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs460234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs461750	0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs464621	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4702633	0.82[AFR][1000 genomes]
rs56344213	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60322708	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs605126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881628	0.85[AFR][1000 genomes]
rs6882326	0.85[AFR][1000 genomes]
rs73051829	0.85[ASN][1000 genomes]
rs7703528	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv1824536	chr5:9539540-9546237	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	esv1817081	chr5:9539540-9546451	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv597074	chr5:9541866-9546412	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv597075	chr5:9542529-9546412	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	esv1803881	chr5:9542529-9546451	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv597076	chr5:9542529-9546451	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs422309	CTD-2001E22.2	cis	Nerve Tibial	GTEx
rs422309	CTD-2001E22.2	cis	Heart Left Ventricle	GTEx
rs422309	CTD-2001E22.2	cis	Muscle Skeletal	GTEx
rs422309	CTD-2001E22.2	cis	lung	GTEx
rs422309	CTD-2001E22.2	cis	Esophagus Mucosa	GTEx
rs422309	CTD-2001E22.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9529600-9544400	Weak transcription	Pancreas	Pancrea
3	chr5:9529600-9544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:9530200-9544600	Weak transcription	Lung	lung
5	chr5:9530400-9544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:9538000-9544400	Weak transcription	Liver	Liver
7	chr5:9538600-9544400	Weak transcription	Left Ventricle	heart
8	chr5:9539400-9544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:9541000-9544400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:9542800-9547200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr5:9542800-9548400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:9543000-9544600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:9543000-9545000	Active TSS	Brain Germinal Matrix	brain
14	chr5:9543000-9545200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:9543000-9547200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:9543000-9547200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:9543000-9547800	Active TSS	Brain Hippocampus Middle	brain
18	chr5:9543000-9548200	Active TSS	Aorta	Aorta
19	chr5:9543200-9544400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:9543200-9544600	Active TSS	Fetal Muscle Trunk	muscle
21	chr5:9543200-9545400	Active TSS	Brain Anterior Caudate	brain
22	chr5:9543200-9547200	Active TSS	Brain Angular Gyrus	brain
23	chr5:9543200-9547400	Active TSS	Right Ventricle	heart
24	chr5:9543200-9548200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:9543200-9548200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr5:9543200-9548200	Active TSS	Right Atrium	heart
27	chr5:9543400-9544400	Flanking Active TSS	Osteobl	bone
28	chr5:9543400-9544800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:9543400-9548000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:9543400-9548400	Active TSS	NHLF	lung
31	chr5:9543600-9544800	Active TSS	Rectal Smooth Muscle	rectum
32	chr5:9543600-9547200	Active TSS	Fetal Intestine Large	intestine
33	chr5:9543600-9548400	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr5:9543800-9544400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:9543800-9544800	Active TSS	Fetal Muscle Leg	muscle
36	chr5:9543800-9547800	Active TSS	Fetal Lung	lung
37	chr5:9543800-9548000	Active TSS	Fetal Heart	heart
38	chr5:9543800-9548200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:9543800-9548200	Active TSS	Fetal Kidney	kidney
40	chr5:9543800-9548600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:9543800-9548800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:9543800-9548800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr5:9544000-9544400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:9544000-9544400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:9544000-9544400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:9544000-9544400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr5:9544000-9544400	Active TSS	NH-A	brain
48	chr5:9544000-9544600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:9544000-9544600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr5:9544000-9544600	Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links