Variant report

Variant	rs16974141
Chromosome Location	chr19:38085648-38085649
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	CHD2	chr19:38084935-38086215	GM12878	blood:	n/a	n/a
2	MYC	chr19:38085116-38086307	K562	blood:	n/a	n/a
3	POLR2A	chr19:38085097-38085683	GM12878	blood:	n/a	n/a
4	IRF1	chr19:38085457-38085983	K562	blood:	n/a	n/a
5	SIX5	chr19:38085571-38085853	H1-hESC	embryonic stem cell:	n/a	chr19:38085724-38085733 chr19:38085722-38085731 chr19:38085721-38085735
6	FOSL2	chr19:38085385-38085961	A549	lung:	n/a	n/a
7	POLR2A	chr19:38085017-38085872	PANC-1	pancreas:	n/a	n/a
8	SP1	chr19:38084986-38085943	A549	lung:	n/a	chr19:38085423-38085433 chr19:38085423-38085433
9	HEY1	chr19:38085417-38085731	K562	blood:	n/a	n/a
10	IRF4	chr19:38085236-38085685	GM12878	blood:	n/a	n/a
11	IRF4	chr19:38085224-38085650	GM12878	blood:	n/a	n/a
12	STAT3	chr19:38084995-38085876	MCF10A-Er-Src	breast:	n/a	chr19:38085558-38085569
13	POLR2A	chr19:38085259-38085860	GM12878	blood:	n/a	n/a
14	ZKSCAN1	chr19:38084992-38086515	Hela-S3	cervix:	n/a	n/a
15	MAX	chr19:38084948-38086359	MCF-7	breast:	n/a	n/a
16	WRNIP1	chr19:38085316-38086067	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:38084964-38086230	GM12891	blood:	n/a	n/a
18	MAX	chr19:38084922-38086300	K562	blood:	n/a	n/a
19	POLR2A	chr19:38085155-38085779	H1-hESC	embryonic stem cell:	n/a	n/a
20	CCNT2	chr19:38085544-38086099	K562	blood:	n/a	n/a
21	POLR2A	chr19:38085113-38086710	H1-neurons	neurons:	n/a	n/a
22	BHLHE40	chr19:38085064-38085851	K562	blood:	n/a	n/a
23	EGR1	chr19:38085218-38085856	MCF-7	breast:	n/a	chr19:38085710-38085734 chr19:38085630-38085641 chr19:38085426-38085435 chr19:38085624-38085646 chr19:38085630-38085640 chr19:38085424-38085439 chr19:38085628-38085642 chr19:38085628-38085643 chr19:38085629-38085642 chr19:38085626-38085640 chr19:38085629-38085642 chr19:38085629-38085642
24	TCF12	chr19:38085032-38086046	ECC-1	luminal epithelium:	n/a	chr19:38085160-38085167
25	ETS1	chr19:38084999-38086036	A549	lung:	n/a	chr19:38085722-38085735
26	RFX5	chr19:38085446-38086271	GM12878	blood:	n/a	chr19:38085696-38085710
27	MYC	chr19:38085547-38085776	HepG2	liver:	n/a	n/a
28	RCOR1	chr19:38085029-38086020	GM12878	blood:	n/a	n/a
29	YY1	chr19:38085132-38085660	GM12891	blood:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
30	JUND	chr19:38084970-38086143	H1-hESC	embryonic stem cell:	n/a	n/a
31	CREB1	chr19:38085065-38085935	A549	lung:	n/a	n/a
32	CEBPD	chr19:38085478-38085772	HepG2	liver:	n/a	n/a
33	CEBPB	chr19:38085410-38085755	HepG2	liver:	n/a	n/a
34	ELK1	chr19:38085056-38086209	GM12878	blood:	n/a	n/a
35	ZNF143	chr19:38085176-38086186	GM12878	blood:	n/a	chr19:38085715-38085733 chr19:38085722-38085731 chr19:38085724-38085733
36	MAX	chr19:38085072-38086328	H1-hESC	embryonic stem cell:	n/a	n/a
37	TEAD4	chr19:38085467-38086224	H1-hESC	embryonic stem cell:	n/a	n/a
38	CEBPB	chr19:38085307-38085882	MCF-7	breast:	n/a	n/a
39	YY1	chr19:38085104-38085888	ECC-1	luminal epithelium:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
40	SIN3AK20	chr19:38085320-38085837	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:38085151-38085851	MCF-7	breast:	n/a	n/a
42	YY1	chr19:38085097-38086257	GM12892	blood:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
43	PBX3	chr19:38085505-38085658	GM12878	blood:	n/a	n/a
44	MYC	chr19:38085163-38085799	MCF-7	breast:	n/a	n/a
45	CEBPD	chr19:38085415-38085723	K562	blood:	n/a	n/a
46	E2F4	chr19:38085217-38085781	MCF10A-Er-Src	breast:	n/a	n/a
47	YY1	chr19:38085211-38085864	SK-N-SH_RA	brain:	n/a	chr19:38085253-38085264 chr19:38085253-38085262
48	MYC	chr19:38085215-38086176	K562	blood:	n/a	n/a
49	ZNF143	chr19:38085231-38086178	H1-hESC	embryonic stem cell:	n/a	chr19:38085715-38085733 chr19:38085722-38085731 chr19:38085724-38085733
50	MYC	chr19:38085029-38086325	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38084603..38087452-chr19:38269351..38271925,3	MCF-7	breast:
2	chr19:38083812..38086216-chr19:38209948..38211806,2	MCF-7	breast:
3	chr19:38085182..38087082-chr19:38268049..38270346,2	K562	blood:
4	chr19:38083338..38085691-chr19:38270478..38272116,2	K562	blood:

Variant related genes	Relation type
ZNF540	TF binding region
ZNF571	TF binding region
ENSG00000198182	Chromatin interaction
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16973544	1.00[AMR][1000 genomes]
rs16973893	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16974028	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16974142	1.00[AMR][1000 genomes]
rs17305823	1.00[YRI][hapmap]
rs2112924	1.00[AMR][1000 genomes]
rs35153242	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38084400-38086000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:38084400-38086200	Active TSS	NHEK	skin
3	chr19:38084400-38086400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:38084400-38086400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:38084600-38085800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:38084600-38086000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:38084600-38086000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:38084600-38086000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:38084600-38086000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:38084600-38086000	Active TSS	K562	blood
11	chr19:38084600-38086200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:38084600-38086200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:38084600-38086200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:38084600-38086200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:38084600-38086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:38084600-38086400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:38084600-38086400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr19:38084600-38086400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:38084600-38086400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:38084600-38086400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr19:38084600-38086400	Active TSS	Colon Smooth Muscle	Colon
22	chr19:38084600-38086400	Active TSS	Esophagus	oesophagus
23	chr19:38084600-38086400	Active TSS	Fetal Kidney	kidney
24	chr19:38084600-38086400	Active TSS	Fetal Stomach	stomach
25	chr19:38084600-38086600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:38084600-38086600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr19:38084600-38086600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:38084600-38086600	Active TSS	Colonic Mucosa	Colon
29	chr19:38084600-38086600	Active TSS	Fetal Intestine Small	intestine
30	chr19:38084600-38086600	Active TSS	HSMM	muscle
31	chr19:38084600-38086600	Active TSS	NHLF	lung
32	chr19:38084600-38086800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:38084600-38086800	Active TSS	Fetal Intestine Large	intestine
34	chr19:38084600-38086800	Active TSS	HMEC	breast
35	chr19:38084600-38087000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:38084800-38086000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:38084800-38086000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38084800-38086000	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr19:38084800-38086200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr19:38084800-38086200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr19:38084800-38086400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr19:38084800-38086400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:38084800-38086400	Active TSS	Fetal Muscle Trunk	muscle
44	chr19:38084800-38086400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:38084800-38086400	Active TSS	Stomach Mucosa	stomach
46	chr19:38084800-38086600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:38084800-38086600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:38084800-38086600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:38084800-38086600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38084800-38086600	Active TSS	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links