Variant report

Variant	rs229653
Chromosome Location	chr14:65203499-65203500
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	CTCF	chr14:65203495-65203524	Kidney_OC	kidney:	n/a	n/a
2	ESR1	chr14:65203174-65203861	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr14:65203204-65203834	ECC-1	luminal epithelium:	n/a	n/a
4	EGR1	chr14:65203207-65203867	ECC-1	luminal epithelium:	n/a	n/a
5	HNF4G	chr14:65203214-65203576	HepG2	liver:	n/a	chr14:65203466-65203478 chr14:65203465-65203473 chr14:65203464-65203479 chr14:65203464-65203479 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203465-65203478 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203464-65203479
6	TEAD4	chr14:65203105-65203926	ECC-1	luminal epithelium:	n/a	n/a
7	HNF4A	chr14:65203305-65203693	HepG2	liver:	n/a	chr14:65203466-65203478 chr14:65203465-65203473 chr14:65203464-65203479 chr14:65203464-65203479 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203465-65203478 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203464-65203479
8	YY1	chr14:65203108-65203850	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr14:65203076-65203899	ECC-1	luminal epithelium:	n/a	n/a
10	YY1	chr14:65203085-65203861	ECC-1	luminal epithelium:	n/a	n/a
11	SIN3A	chr14:65203109-65203764	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr14:65203086-65203930	ECC-1	luminal epithelium:	n/a	n/a
13	RAD21	chr14:65203056-65203769	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr14:65203006-65204001	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr14:65203006-65203911	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr14:65203102-65203679	K562	blood:	n/a	n/a
17	CTCF	chr14:65203402-65203582	HepG2	liver:	n/a	n/a
18	ZNF143	chr14:65203131-65203786	H1-hESC	embryonic stem cell:	n/a	chr14:65203304-65203323 chr14:65203305-65203320
19	EGR1	chr14:65203349-65203836	ECC-1	luminal epithelium:	n/a	n/a
20	EP300	chr14:65202897-65205567	ECC-1	luminal epithelium:	n/a	n/a
21	EP300	chr14:65203088-65203880	ECC-1	luminal epithelium:	n/a	n/a
22	ZBTB7A	chr14:65202941-65205411	ECC-1	luminal epithelium:	n/a	chr14:65205006-65205014 chr14:65204275-65204283
23	NR3C1	chr14:65203104-65203732	ECC-1	luminal epithelium:	n/a	n/a
24	HNF4A	chr14:65203252-65203618	HepG2	liver:	n/a	chr14:65203466-65203478 chr14:65203465-65203473 chr14:65203464-65203479 chr14:65203464-65203479 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203465-65203478 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203464-65203479
25	ESR1	chr14:65203196-65203754	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr14:65202973-65203890	ECC-1	luminal epithelium:	n/a	chr14:65203307-65203316
27	USF1	chr14:65203122-65203815	ECC-1	luminal epithelium:	n/a	n/a
28	CEBPB	chr14:65203080-65203788	ECC-1	luminal epithelium:	n/a	chr14:65203481-65203489 chr14:65203304-65203315
29	NFIC	chr14:65202879-65203979	ECC-1	luminal epithelium:	n/a	n/a
30	HNF4A	chr14:65203264-65203654	HepG2	liver:	n/a	chr14:65203466-65203478 chr14:65203465-65203473 chr14:65203464-65203479 chr14:65203464-65203479 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203465-65203478 chr14:65203466-65203478 chr14:65203464-65203479 chr14:65203464-65203479
31	POLR2A	chr14:65203095-65203682	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr14:65203440-65203590	NHEK	skin:	n/a	n/a
33	MAX	chr14:65203077-65203945	ECC-1	luminal epithelium:	n/a	chr14:65203307-65203316
34	ESR1	chr14:65203176-65203860	ECC-1	luminal epithelium:	n/a	n/a
35	ZBTB7A	chr14:65202967-65205326	ECC-1	luminal epithelium:	n/a	chr14:65205006-65205014 chr14:65204275-65204283
36	USF1	chr14:65203280-65203875	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr14:65203240-65203510	SAEC	small airway:	n/a	n/a
38	CTCF	chr14:65203417-65203528	Pancreas_OC	pancreas:	n/a	n/a
39	CTCF	chr14:65203468-65203526	HepG2	liver:	n/a	n/a
40	FOXM1	chr14:65203184-65203901	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr14:65203460-65203524	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr14:65203415-65203599	NHEK	skin:	n/a	n/a
43	ZBTB7A	chr14:65203333-65203529	HepG2	liver:	n/a	n/a
44	TCF12	chr14:65202990-65204052	ECC-1	luminal epithelium:	n/a	chr14:65203290-65203300
45	TCF12	chr14:65202903-65204057	ECC-1	luminal epithelium:	n/a	chr14:65203290-65203300
46	FOXM1	chr14:65203027-65203904	ECC-1	luminal epithelium:	n/a	n/a
47	CEBPB	chr14:65203107-65203504	ECC-1	luminal epithelium:	n/a	chr14:65203481-65203489 chr14:65203304-65203315
48	RAD21	chr14:65202935-65203847	H1-hESC	embryonic stem cell:	n/a	n/a
49	ESR1	chr14:65203250-65203569	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65202287..65204221-chr14:65212504..65215467,2	MCF-7	breast:
2	chr14:65160629..65162751-chr14:65201298..65203943,2	MCF-7	breast:

Variant related genes	Relation type
PLEKHG3	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10138034	0.96[EUR][1000 genomes]
rs11621159	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621379	0.89[EUR][1000 genomes]
rs11622754	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11625500	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628301	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883289	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884903	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12892852	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895353	1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553163	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs170683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767074	1.00[YRI][hapmap]
rs229622	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229645	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs229648	1.00[ASN][1000 genomes]
rs229649	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229656	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34340219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140781	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71420472	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732311	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943995	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];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	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv902023	chr14:65200821-65243885	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv902024	chr14:65200821-65244950	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65184000-65208800	Weak transcription	Fetal Brain Male	brain
2	chr14:65189800-65207000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:65192400-65210400	Weak transcription	Osteobl	bone
4	chr14:65193200-65212200	Weak transcription	Fetal Heart	heart
5	chr14:65193400-65212400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:65193400-65212400	Weak transcription	HSMMtube	muscle
7	chr14:65193600-65209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:65193600-65212800	Weak transcription	HUVEC	blood vessel
9	chr14:65193800-65212200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:65193800-65214400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr14:65194000-65209000	Weak transcription	Small Intestine	intestine
12	chr14:65194200-65204800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:65194200-65216200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr14:65195000-65207200	Weak transcription	Primary B cells from cord blood	blood
15	chr14:65196000-65208200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:65196600-65212200	Weak transcription	NHLF	lung
17	chr14:65197200-65206000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:65198000-65214800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:65199000-65205200	Weak transcription	NH-A	brain
20	chr14:65199600-65207800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:65199800-65203800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:65199800-65205200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:65199800-65205600	Weak transcription	Fetal Lung	lung
24	chr14:65200200-65204400	Genic enhancers	Brain Hippocampus Middle	brain
25	chr14:65200400-65205400	Weak transcription	Brain Germinal Matrix	brain
26	chr14:65200400-65207600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr14:65200600-65203800	Genic enhancers	Adipose Nuclei	Adipose
28	chr14:65200600-65204400	Weak transcription	Left Ventricle	heart
29	chr14:65200600-65206000	Weak transcription	Fetal Brain Female	brain
30	chr14:65200800-65204400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:65201000-65221800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr14:65201400-65212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr14:65201600-65204200	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr14:65201800-65204400	Genic enhancers	Rectal Mucosa Donor 31	rectum
35	chr14:65201800-65204600	Genic enhancers	Fetal Intestine Small	intestine
36	chr14:65202200-65204200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr14:65202200-65204400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:65202200-65204400	Genic enhancers	Fetal Intestine Large	intestine
39	chr14:65202200-65205400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:65202200-65211200	Strong transcription	Ovary	ovary
41	chr14:65202200-65217400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:65202400-65203800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr14:65202400-65204000	Genic enhancers	NHEK	skin
44	chr14:65202400-65212000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr14:65202600-65204200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:65202600-65211200	Weak transcription	Fetal Thymus	thymus
47	chr14:65202600-65211400	Strong transcription	Rectal Smooth Muscle	rectum
48	chr14:65202800-65203600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr14:65202800-65203600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr14:65202800-65203800	Genic enhancers	H1 Cell Line	embryonic stem cell

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