Variant report

Variant	rs74077638
Chromosome Location	chr13:49067238-49067239
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	RELA	chr13:49066262-49067756	GM10847	blood:	n/a	n/a
2	WRNIP1	chr13:49067074-49067244	GM12878	blood:	n/a	n/a
3	GATA1	chr13:49066497-49067256	PBDE	blood:	n/a	n/a
4	RELA	chr13:49065647-49067778	GM19099	blood:	n/a	n/a
5	POLR2A	chr13:49063049-49067797	GM12892	blood:	n/a	n/a
6	POLR2A	chr13:49065667-49067247	PBDE	blood:	n/a	n/a
7	POLR2A	chr13:49063878-49067866	GM19193	blood:	n/a	n/a
8	RELA	chr13:49065483-49067807	GM15510	blood:	n/a	n/a
9	RUNX3	chr13:49067157-49067841	GM12878	blood:	n/a	n/a
10	MTA3	chr13:49066009-49067680	GM12878	blood:	n/a	n/a
11	RELA	chr13:49066105-49067800	GM18951	blood:	n/a	n/a
12	POLR2A	chr13:49063103-49067843	GM12878	blood:	n/a	n/a
13	RCOR1	chr13:49066636-49067318	GM12878	blood:	n/a	n/a
14	IKZF1	chr13:49066198-49067298	GM12878	blood:	n/a	n/a
15	POLR2A	chr13:49060366-49068321	GM12891	blood:	n/a	n/a
16	POLR2A	chr13:49063167-49068417	GM19099	blood:	n/a	n/a
17	POLR2A	chr13:49063104-49067911	GM18951	blood:	n/a	n/a
18	POLR2A	chr13:49062513-49068209	GM18505	blood:	n/a	n/a
19	SMC3	chr13:49066731-49067365	GM12878	blood:	n/a	n/a
20	ZZZ3	chr13:49067217-49067622	GM12878	blood:	n/a	n/a
21	RELA	chr13:49065544-49067468	GM18505	blood:	n/a	n/a
22	RELA	chr13:49066142-49067876	GM19193	blood:	n/a	n/a
23	NFIC	chr13:49066253-49067407	GM12878	blood:	n/a	n/a
24	POLR2A	chr13:49064622-49067847	GM18526	blood:	n/a	n/a

Variant related genes	Relation type
RCBTB2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12583617	1.00[EUR][1000 genomes]
rs12583644	1.00[EUR][1000 genomes]
rs12583787	1.00[ASN][1000 genomes]
rs12585384	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585742	1.00[EUR][1000 genomes]
rs12857866	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071937	1.00[ASN][1000 genomes]
rs2148515	1.00[ASN][1000 genomes]
rs4151472	1.00[EUR][1000 genomes]
rs4151479	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4151522	0.86[AFR][1000 genomes]
rs4151524	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4151598	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151602	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449268	1.00[ASN][1000 genomes]
rs55686933	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57394470	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650379	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139763	1.00[ASN][1000 genomes]
rs7319276	1.00[ASN][1000 genomes]
rs7326934	1.00[ASN][1000 genomes]
rs73479216	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73479220	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074915	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074916	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074942	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074946	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74075993	0.83[AFR][1000 genomes]
rs9316384	1.00[ASN][1000 genomes]
rs9316386	1.00[ASN][1000 genomes]
rs9316387	1.00[ASN][1000 genomes]
rs9316396	1.00[ASN][1000 genomes]
rs9316398	1.00[ASN][1000 genomes]
rs9331984	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331994	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332033	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332044	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332055	1.00[ASN][1000 genomes]
rs9332070	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332085	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591176	1.00[ASN][1000 genomes]
rs9595914	1.00[ASN][1000 genomes]
rs9595924	1.00[ASN][1000 genomes]
rs9595926	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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 lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv3384312	chr13:49063851-49067249	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 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	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:49032400-49067400	Weak transcription	Pancreas	Pancrea
5	chr13:49032400-49067600	Weak transcription	Gastric	stomach
6	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
7	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
8	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:49057400-49068400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:49060600-49067400	Weak transcription	Stomach Mucosa	stomach
12	chr13:49061400-49072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:49062600-49070800	Weak transcription	Fetal Brain Male	brain
14	chr13:49062800-49067400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:49062800-49070400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr13:49062800-49072000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:49063000-49067400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr13:49063000-49068000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:49063200-49067400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr13:49063200-49071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:49063600-49067600	Weak transcription	Brain Germinal Matrix	brain
23	chr13:49064200-49068200	Flanking Active TSS	GM12878-XiMat	blood
24	chr13:49064200-49069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:49064200-49075200	Weak transcription	Fetal Intestine Large	intestine
26	chr13:49064400-49068000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr13:49064400-49068800	Flanking Active TSS	Dnd41	blood
28	chr13:49064600-49070600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:49064800-49071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:49065000-49069800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:49065000-49070200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr13:49065400-49067400	Flanking Active TSS	NHDF-Ad	bronchial
33	chr13:49065400-49069400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:49065400-49072000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:49065600-49067400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr13:49065600-49069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr13:49066200-49067400	Flanking Active TSS	Osteobl	bone
38	chr13:49066200-49067800	Enhancers	Spleen	Spleen
39	chr13:49066200-49068200	Enhancers	Lung	lung
40	chr13:49066400-49067800	Enhancers	Fetal Heart	heart
41	chr13:49066400-49068000	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr13:49066400-49068000	Strong transcription	Fetal Brain Female	brain
43	chr13:49066600-49067800	Enhancers	Placenta	Placenta
44	chr13:49066600-49067800	Enhancers	Right Ventricle	heart
45	chr13:49066600-49069000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr13:49066800-49067600	Weak transcription	Fetal Muscle Leg	muscle
47	chr13:49066800-49067600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr13:49066800-49067800	Enhancers	Primary B cells from peripheral blood	blood
49	chr13:49066800-49067800	Genic enhancers	Fetal Stomach	stomach
50	chr13:49066800-49073200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links