Variant report

Variant	rs10421768
Chromosome Location	chr19:35772899-35772900
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	SPI1	chr19:35772895-35773263	GM12891	blood:	n/a	chr19:35773138-35773151 chr19:35773072-35773081 chr19:35773070-35773083
2	POLR2A	chr19:35772866-35773505	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:35772824-35773108	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr19:35772831-35773488	K562	blood:	n/a	chr19:35772896-35772905 chr19:35772897-35772904
5	BHLHE40	chr19:35772871-35773341	K562	blood:	n/a	chr19:35773030-35773046
6	SPI1	chr19:35772830-35773342	HL-60	blood:	n/a	chr19:35773138-35773151 chr19:35773072-35773081 chr19:35773070-35773083
7	NFATC1	chr19:35772664-35773306	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:35772807-35772906	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:35772786-35773644	K562	blood:	n/a	n/a
10	PML	chr19:35772781-35773247	GM12878	blood:	n/a	n/a
11	ELF1	chr19:35772739-35773334	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:35772846-35773425	HL-60	blood:	n/a	n/a
13	NFIC	chr19:35772885-35773196	GM12878	blood:	n/a	n/a
14	SPI1	chr19:35772894-35773203	GM12878	blood:	n/a	chr19:35773138-35773151 chr19:35773072-35773081 chr19:35773070-35773083
15	SPI1	chr19:35772840-35773424	HL-60	blood:	n/a	chr19:35773138-35773151 chr19:35773363-35773376 chr19:35773072-35773081 chr19:35773070-35773083
16	POLR2A	chr19:35772857-35773796	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:35772880-35773312	K562	blood:	n/a	n/a
18	MTA3	chr19:35772710-35773498	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:35772873-35773474	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:35772884-35773255	K562	blood:	n/a	n/a
21	POLR2A	chr19:35772843-35774627	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:35771719..35773722-chr19:35808312..35810561,2	K562	blood:
2	chr19:35758290..35762202-chr19:35770035..35773582,5	K562	blood:
3	chr19:35772633..35774155-chr19:36132847..36134898,2	MCF-7	breast:
4	chr19:35769830..35774693-chr19:35781606..35784141,6	K562	blood:

Variant related genes	Relation type
HAMP	TF binding region
ENSG00000012124	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000105695	Chromatin interaction
ENSG00000105672	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10405246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419261	1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419959	0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10421096	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421504	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424619	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973672	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979058	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979792	0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981527	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984022	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985618	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986033	1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345192	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073899	0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280744	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280745	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365133	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250673	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497966	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35959789	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112772	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71352913	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256866	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101606	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS 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	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS 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 miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
10	nsv911622	chr19:35752917-35773146	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
11	nsv911623	chr19:35752917-35775441	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10421768	SERTAD3	cis	cerebellum	SCAN
rs10421768	PHLDB3	cis	cerebellum	SCAN
rs10421768	U2AF1L4	cis	lymphoblastoid	seeQTL
rs10421768	ZFP36	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35761400-35775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:35762800-35780000	Weak transcription	Hela-S3	cervix
3	chr19:35763600-35773400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:35767800-35775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:35768200-35775600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:35768400-35773400	Weak transcription	Small Intestine	intestine
7	chr19:35768400-35781400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:35768800-35781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:35769200-35775600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:35769800-35775600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:35770000-35775600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:35770000-35775800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:35770200-35773000	Enhancers	HepG2	liver
14	chr19:35770200-35773000	Weak transcription	HMEC	breast
15	chr19:35770200-35775400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:35770200-35775600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:35770400-35776800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:35770600-35773000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:35770600-35773000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:35770600-35773000	Weak transcription	Left Ventricle	heart
21	chr19:35770600-35773200	Weak transcription	Gastric	stomach
22	chr19:35770600-35773400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:35770600-35773600	Enhancers	Fetal Lung	lung
24	chr19:35770800-35773600	Enhancers	Spleen	Spleen
25	chr19:35770800-35775400	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:35771000-35773000	Weak transcription	Fetal Intestine Large	intestine
27	chr19:35771000-35773200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:35771000-35773200	Weak transcription	Brain Germinal Matrix	brain
29	chr19:35771000-35773400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr19:35771000-35773600	Enhancers	GM12878-XiMat	blood
31	chr19:35771000-35773800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:35771000-35774600	Enhancers	Primary B cells from cord blood	blood
33	chr19:35771200-35773000	Weak transcription	Right Ventricle	heart
34	chr19:35771200-35773400	Enhancers	Pancreas	Pancrea
35	chr19:35771200-35775000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:35771400-35773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:35771400-35773400	Enhancers	Esophagus	oesophagus
38	chr19:35771600-35773200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr19:35771800-35776200	Weak transcription	Fetal Kidney	kidney
40	chr19:35772000-35773000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:35772000-35773000	Enhancers	NHEK	skin
42	chr19:35772000-35773600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:35772000-35774000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr19:35772000-35775600	Weak transcription	Brain Angular Gyrus	brain
45	chr19:35772000-35775600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:35772000-35781200	Weak transcription	Brain Substantia Nigra	brain
47	chr19:35772200-35773000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:35772200-35773400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:35772200-35774400	Weak transcription	Ovary	ovary
50	chr19:35772400-35773000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links