Variant report

Variant	rs862460
Chromosome Location	chr19:39343904-39343905
allele	C/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	BCL3	chr19:39338958-39343958	A549	lung:	n/a	chr19:39343210-39343219 chr19:39341504-39341513 chr19:39340067-39340080 chr19:39342053-39342066 chr19:39340700-39340713 chr19:39343077-39343090 chr19:39343075-39343088 chr19:39343069-39343082 chr19:39340693-39340706 chr19:39340664-39340673 chr19:39342783-39342796 chr19:39339897-39339906
2	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr19:39342961-39343906	A549	lung:	n/a	n/a
4	TCF12	chr19:39342952-39344010	A549	lung:	n/a	n/a
5	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
7	YY1	chr19:39342801-39343918	A549	lung:	n/a	chr19:39343211-39343220 chr19:39343067-39343078 chr19:39343208-39343219 chr19:39343079-39343090
8	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
10	MAZ	chr19:39339527-39343946	IMR90	lung:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39342573-39342586 chr19:39342574-39342585
11	SP1	chr19:39339150-39343979	A549	lung:	n/a	chr19:39343001-39343013 chr19:39342682-39342691 chr19:39341185-39341194 chr19:39341870-39341879 chr19:39341186-39341199 chr19:39342556-39342565 chr19:39340203-39340217 chr19:39342554-39342566 chr19:39340202-39340214 chr19:39341274-39341286 chr19:39341185-39341195 chr19:39341040-39341049 chr19:39341276-39341285 chr19:39343209-39343221 chr19:39340202-39340214 chr19:39342556-39342565 chr19:39342555-39342564 chr19:39341185-39341194 chr19:39342683-39342692 chr19:39343210-39343219 chr19:39342551-39342564 chr19:39340941-39340952 chr19:39342475-39342484 chr19:39342554-39342566 chr19:39343008-39343017 chr19:39342555-39342565 chr19:39343006-39343018 chr19:39342619-39342631 chr19:39341039-39341051 chr19:39341184-39341196 chr19:39343210-39343220 chr19:39340951-39340972 chr19:39342662-39342671 chr19:39342554-39342565 chr19:39343006-39343018 chr19:39343211-39343220 chr19:39340203-39340213 chr19:39342658-39342672 chr19:39341039-39341051 chr19:39341186-39341195 chr19:39342555-39342565 chr19:39340204-39340213 chr19:39342621-39342630 chr19:39340942-39340956 chr19:39342619-39342631 chr19:39341184-39341196 chr19:39343209-39343221 chr19:39343001-39343013 chr19:39343210-39343224 chr19:39342998-39343012 chr19:39340626-39340647 chr19:39341274-39341286 chr19:39340203-39340212
12	GATA3	chr19:39339013-39344076	A549	lung:	n/a	chr19:39343447-39343456
13	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
14	PBX3	chr19:39342233-39343965	A549	lung:	n/a	n/a
15	SP1	chr19:39339038-39344135	A549	lung:	n/a	chr19:39343001-39343013 chr19:39342682-39342691 chr19:39341185-39341194 chr19:39341870-39341879 chr19:39341186-39341199 chr19:39342556-39342565 chr19:39340203-39340217 chr19:39342554-39342566 chr19:39340202-39340214 chr19:39341274-39341286 chr19:39341185-39341195 chr19:39341040-39341049 chr19:39341276-39341285 chr19:39343209-39343221 chr19:39340202-39340214 chr19:39342556-39342565 chr19:39342555-39342564 chr19:39341185-39341194 chr19:39342683-39342692 chr19:39343210-39343219 chr19:39342551-39342564 chr19:39340941-39340952 chr19:39342475-39342484 chr19:39342554-39342566 chr19:39343008-39343017 chr19:39342555-39342565 chr19:39343006-39343018 chr19:39342619-39342631 chr19:39341039-39341051 chr19:39341184-39341196 chr19:39343210-39343220 chr19:39340951-39340972 chr19:39342662-39342671 chr19:39342554-39342565 chr19:39343006-39343018 chr19:39343211-39343220 chr19:39340203-39340213 chr19:39342658-39342672 chr19:39341039-39341051 chr19:39341186-39341195 chr19:39342555-39342565 chr19:39340204-39340213 chr19:39342621-39342630 chr19:39340942-39340956 chr19:39342619-39342631 chr19:39341184-39341196 chr19:39343209-39343221 chr19:39343001-39343013 chr19:39343210-39343224 chr19:39342998-39343012 chr19:39340626-39340647 chr19:39341274-39341286 chr19:39340203-39340212
16	BCL3	chr19:39342036-39343913	A549	lung:	n/a	chr19:39343210-39343219 chr19:39342053-39342066 chr19:39343077-39343090 chr19:39343075-39343088 chr19:39343069-39343082 chr19:39342783-39342796
17	EP300	chr19:39339022-39343992	A549	lung:	n/a	chr19:39342120-39342134 chr19:39341504-39341518 chr19:39341267-39341283 chr19:39340665-39340674 chr19:39340069-39340085
18	POLR2A	chr19:39339810-39343907	MCF-7	breast:	n/a	n/a
19	RCOR1	chr19:39342918-39343918	IMR90	lung:	n/a	n/a
20	PBX3	chr19:39342257-39343909	A549	lung:	n/a	n/a
21	SIN3AK20	chr19:39342839-39344043	A549	lung:	n/a	n/a
22	POLR2A	chr19:39337675-39343938	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD1	chr19:39338427-39343932	IMR90	lung:	n/a	chr19:39340621-39340631 chr19:39342661-39342671
24	SIX5	chr19:39337474-39344181	A549	lung:	n/a	n/a
25	ATF3	chr19:39342880-39344202	A549	lung:	n/a	chr19:39343211-39343220
26	MAX	chr19:39339105-39343956	A549	lung:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
27	MYC	chr19:39338383-39344059	A549	lung:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39338398-39338407 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
28	MAX	chr19:39338946-39344108	A549	lung:	n/a	chr19:39342575-39342584 chr19:39342576-39342583 chr19:39342574-39342585 chr19:39342575-39342584 chr19:39343002-39343012 chr19:39342575-39342585 chr19:39342574-39342584 chr19:39342566-39342582 chr19:39342573-39342586 chr19:39340626-39340636 chr19:39342573-39342583 chr19:39342573-39342586 chr19:39342574-39342585
29	MXI1	chr19:39341209-39343964	IMR90	lung:	n/a	n/a
30	REST	chr19:39342840-39343957	A549	lung:	n/a	chr19:39342999-39343012

No.	Distal block	Cell Line	Cell type
1	chr19:39341886..39344706-chr19:39358962..39361932,2	K562	blood:
2	chr19:39341787..39344352-chr19:39369532..39371797,3	MCF-7	breast:
3	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
4	chr19:39341602..39344396-chr19:39810637..39813386,2	K562	blood:
5	chr19:39337733..39344793-chr19:39358054..39362711,15	MCF-7	breast:
6	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
7	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
8	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:
9	chr19:39343341..39344893-chr19:39367405..39369685,2	K562	blood:
10	chr19:39340592..39344706-chr19:39357882..39361932,6	K562	blood:
11	chr19:39225241..39228879-chr19:39342547..39344492,3	K562	blood:
12	chr19:39341689..39344249-chr19:40949611..40951303,2	K562	blood:
13	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
14	chr19:39137047..39143767-chr19:39341076..39344906,12	MCF-7	breast:
15	chr19:39339114..39344809-chr19:39363672..39368217,5	MCF-7	breast:
16	chr19:39108184..39110512-chr19:39341783..39344242,3	MCF-7	breast:
17	chr19:39340906..39344724-chr19:39389015..39390874,4	MCF-7	breast:
18	chr19:39339409..39344372-chr19:39356868..39363816,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NFKBIB-5	chr19:39343580-39344120	NONHSAT066251

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10403012	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411480	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10411844	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10424892	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10425464	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10426289	0.81[CHB][hapmap]
rs1078734	0.83[AMR][1000 genomes]
rs11668179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668766	0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11671711	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12974488	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12977821	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1529713	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2116852	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278010	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35829996	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4328569	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802928	0.85[EUR][1000 genomes]
rs7248208	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8108906	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8110679	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs862454	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862458	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862461	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862462	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862463	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9419	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789283	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs862460	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39339000-39344000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:39339800-39344000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:39339800-39344000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:39340000-39344000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:39342000-39344000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:39342000-39344000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39342000-39344000	Active TSS	Aorta	Aorta
8	chr19:39342200-39344000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39342200-39344000	Active TSS	NHLF	lung
10	chr19:39342400-39344000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:39342600-39344000	Active TSS	A549	lung
12	chr19:39343200-39344000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
13	chr19:39343200-39344000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:39343200-39344000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:39343200-39344000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:39343200-39344000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:39343200-39344000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr19:39343200-39344000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:39343200-39344000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr19:39343200-39344000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr19:39343200-39344000	Flanking Active TSS	K562	blood
22	chr19:39343200-39344000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:39343400-39344000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr19:39343400-39344000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:39343400-39344000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:39343400-39344000	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr19:39343400-39344000	Flanking Active TSS	HSMM	muscle
28	chr19:39343400-39344200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:39343600-39344000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:39343600-39344000	Enhancers	Left Ventricle	heart
31	chr19:39343600-39344000	Enhancers	Stomach Mucosa	stomach
32	chr19:39343600-39344000	Enhancers	Spleen	Spleen
33	chr19:39343600-39344000	Flanking Active TSS	Hela-S3	cervix
34	chr19:39343600-39344000	Active TSS	HepG2	liver
35	chr19:39343600-39348200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
37	chr19:39343800-39344000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:39343800-39344000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:39343800-39344000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:39343800-39344000	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:39343800-39344000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:39343800-39344000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39343800-39344000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr19:39343800-39344000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:39343800-39344000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr19:39343800-39344000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:39343800-39344000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:39343800-39344000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:39343800-39344000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr19:39343800-39344000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links