Variant report

Variant	rs1724121
Chromosome Location	chr2:96808549-96808550
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	POLR2A	chr2:96806481-96811332	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:96806257-96812804	GM15510	blood:	n/a	n/a
3	EGR1	chr2:96807893-96808880	GM12878	blood:	n/a	chr2:96808198-96808207 chr2:96808194-96808209 chr2:96808196-96808207 chr2:96808197-96808207 chr2:96808195-96808208 chr2:96808491-96808501 chr2:96808195-96808208 chr2:96808490-96808501 chr2:96808200-96808210 chr2:96808282-96808297 chr2:96808196-96808207 chr2:96808489-96808503 chr2:96808195-96808209 chr2:96808490-96808501 chr2:96808195-96808208 chr2:96808197-96808207 chr2:96808489-96808502 chr2:96808491-96808501 chr2:96808195-96808208
4	POLR2A	chr2:96808530-96808559	MCF-7	breast:	n/a	n/a
5	NFIC	chr2:96807794-96808623	GM12878	blood:	n/a	n/a
6	YY1	chr2:96807875-96808840	GM12878	blood:	n/a	chr2:96808197-96808211
7	TCF3	chr2:96807813-96809675	GM12878	blood:	n/a	chr2:96808535-96808549 chr2:96808537-96808546
8	POLR2A	chr2:96807638-96809487	H1-hESC	embryonic stem cell:	n/a	n/a
9	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
10	EP300	chr2:96807828-96809199	GM12878	blood:	n/a	n/a
11	BHLHE40	chr2:96807669-96809494	GM12878	blood:	n/a	n/a
12	ZBTB33	chr2:96807731-96808901	GM12878	blood:	n/a	n/a
13	IRF4	chr2:96807810-96808805	GM12878	blood:	n/a	n/a
14	RELA	chr2:96807819-96809239	GM15510	blood:	n/a	n/a
15	TBL1XR1	chr2:96807840-96812802	GM12878	blood:	n/a	n/a
16	CHD2	chr2:96808135-96808791	Hela-S3	cervix:	n/a	n/a
17	NFATC1	chr2:96807447-96810034	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:96806742-96812863	Raji	blood:	n/a	n/a
19	TAF1	chr2:96807918-96808657	GM12891	blood:	n/a	n/a
20	PML	chr2:96806496-96814786	GM12878	blood:	n/a	chr2:96814389-96814398
21	POLR2A	chr2:96807809-96808692	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
23	TAF1	chr2:96807891-96808568	GM12878	blood:	n/a	n/a
24	BHLHE40	chr2:96808500-96808696	K562	blood:	n/a	n/a
25	PAX5	chr2:96807697-96808868	GM12878	blood:	n/a	n/a
26	EGR1	chr2:96808043-96808591	GM12878	blood:	n/a	chr2:96808198-96808207 chr2:96808194-96808209 chr2:96808196-96808207 chr2:96808197-96808207 chr2:96808195-96808208 chr2:96808491-96808501 chr2:96808195-96808208 chr2:96808490-96808501 chr2:96808200-96808210 chr2:96808282-96808297 chr2:96808196-96808207 chr2:96808489-96808503 chr2:96808195-96808209 chr2:96808490-96808501 chr2:96808195-96808208 chr2:96808197-96808207 chr2:96808489-96808502 chr2:96808491-96808501 chr2:96808195-96808208
27	MYC	chr2:96808442-96808558	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:96806166-96813187	GM19193	blood:	n/a	n/a
29	POLR2A	chr2:96805990-96812814	GM12892	blood:	n/a	n/a
30	POU2F2	chr2:96807432-96811594	GM12878	blood:	n/a	n/a
31	REST	chr2:96808442-96808851	GM12878	blood:	n/a	n/a
32	NFATC1	chr2:96806082-96812882	GM12878	blood:	n/a	n/a
33	ZBTB33	chr2:96807796-96808690	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:96807735-96811533	NB4	blood:	n/a	n/a
35	PAX5	chr2:96807520-96810007	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:96797189-96814534	GM12892	blood:	n/a	n/a
37	PML	chr2:96807728-96809348	GM12878	blood:	n/a	n/a
38	CUX1	chr2:96807671-96808931	GM12878	blood:	n/a	n/a
39	BRCA1	chr2:96807827-96811711	GM12878	blood:	n/a	n/a
40	MTA3	chr2:96806625-96815107	GM12878	blood:	n/a	n/a
41	FOXM1	chr2:96807733-96809741	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:96800040-96811369	IMR90	lung:	n/a	n/a
43	ZNF384	chr2:96807796-96808768	GM12878	blood:	n/a	n/a
44	EGR1	chr2:96807896-96808640	GM12878	blood:	n/a	chr2:96808198-96808207 chr2:96808194-96808209 chr2:96808196-96808207 chr2:96808197-96808207 chr2:96808195-96808208 chr2:96808491-96808501 chr2:96808195-96808208 chr2:96808490-96808501 chr2:96808200-96808210 chr2:96808282-96808297 chr2:96808196-96808207 chr2:96808489-96808503 chr2:96808195-96808209 chr2:96808490-96808501 chr2:96808195-96808208 chr2:96808197-96808207 chr2:96808489-96808502 chr2:96808491-96808501 chr2:96808195-96808208
45	SMC3	chr2:96807811-96808595	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:96807671-96812790	GM18526	blood:	n/a	n/a
47	SIN3A	chr2:96807978-96812336	GM12878	blood:	n/a	chr2:96811156-96811169
48	POLR2A	chr2:96806534-96814566	GM12891	blood:	n/a	n/a
49	POLR2A	chr2:96802751-96813556	GM12892	blood:	n/a	n/a
50	YY1	chr2:96807804-96808666	GM12878	blood:	n/a	chr2:96808197-96808211

No.	Distal block	Cell Line	Cell type
1	chr2:96808384..96810178-chr2:96817878..96819438,2	K562	blood:
2	chr1:37940232..37940809-chr2:96808547..96809229,2	Hela-S3	cervix:
3	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:
4	chr1:149858306..149859142-chr2:96808156..96808675,2	Hela-S3	cervix:
5	chr2:96746307..96748974-chr2:96806450..96808767,2	K562	blood:

Variant related genes	Relation type
ASTL	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000184260	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10183151	0.81[EUR][1000 genomes]
rs1030864	0.85[EUR][1000 genomes]
rs1168966	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168967	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1168968	0.85[EUR][1000 genomes]
rs1168970	0.85[EUR][1000 genomes]
rs1168972	0.85[EUR][1000 genomes]
rs1168974	0.85[EUR][1000 genomes]
rs1168975	0.85[EUR][1000 genomes]
rs1168976	0.85[EUR][1000 genomes]
rs13009727	0.82[EUR][1000 genomes]
rs13019188	0.93[EUR][1000 genomes]
rs1657502	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1724125	0.83[EUR][1000 genomes]
rs2252697	0.92[EUR][1000 genomes]
rs2576437	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918916	0.84[EUR][1000 genomes]
rs2969490	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907299	0.80[EUR][1000 genomes]
rs749457	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs749459	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7604842	0.81[EUR][1000 genomes]
rs893173	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
9	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
15	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
18	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
19	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1724121	ADRA2B	cis	Thyroid	GTEx
rs1724121	GPAT2	cis	Muscle Skeletal	GTEx
rs1724121	FAHD2CP	cis	Muscle Skeletal	GTEx
rs1724121	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs1724121	FAHD2CP	cis	lung	GTEx
rs1724121	FAHD2CP	cis	Artery Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96798000-96809400	Weak transcription	Gastric	stomach
2	chr2:96802600-96810200	Weak transcription	HSMMtube	muscle
3	chr2:96803600-96809200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:96804800-96809000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:96804800-96809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:96804800-96809600	Weak transcription	Pancreas	Pancrea
7	chr2:96805000-96809600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:96805200-96808600	Weak transcription	Colonic Mucosa	Colon
9	chr2:96805200-96808800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:96805200-96809200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:96805200-96809400	Weak transcription	Stomach Mucosa	stomach
12	chr2:96805200-96809800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:96805400-96809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:96805400-96809600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:96806800-96808600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:96806800-96810800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr2:96806800-96810800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:96807600-96809000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:96807600-96809600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:96807800-96809600	Enhancers	Esophagus	oesophagus
21	chr2:96807800-96810400	Transcr. at gene 5' and 3'	Thymus	Thymus
22	chr2:96808000-96808800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr2:96808000-96808800	Enhancers	K562	blood
24	chr2:96808000-96809200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:96808000-96809400	Genic enhancers	Spleen	Spleen
26	chr2:96808000-96809800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr2:96808000-96810000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:96808000-96810200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
29	chr2:96808000-96810200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
30	chr2:96808000-96810400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
31	chr2:96808200-96808600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr2:96808200-96809000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:96808200-96809000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:96808200-96809200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr2:96808200-96809600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:96808200-96809600	Strong transcription	Fetal Stomach	stomach
37	chr2:96808200-96809800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
38	chr2:96808200-96809800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr2:96808200-96810000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr2:96808400-96808600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:96808400-96808600	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr2:96808400-96808600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr2:96808400-96808800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:96808400-96808800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:96808400-96808800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:96808400-96808800	Genic enhancers	Right Ventricle	heart
47	chr2:96808400-96809000	Enhancers	Primary hematopoietic stem cells	blood
48	chr2:96808400-96809000	Weak transcription	Dnd41	blood
49	chr2:96808400-96809200	Enhancers	Primary B cells from cord blood	blood
50	chr2:96808400-96809200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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