Variant report

Variant	rs246138
Chromosome Location	chr16:69478526-69478527
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	IRF1	chr16:69477950-69479275	K562	blood:	n/a	chr16:69478895-69478905 chr16:69478893-69478906 chr16:69478440-69478453 chr16:69478893-69478906 chr16:69478434-69478454 chr16:69478440-69478453 chr16:69478437-69478448 chr16:69478889-69478910 chr16:69478892-69478906 chr16:69478142-69478156 chr16:69478895-69478906 chr16:69478894-69478911 chr16:69478438-69478452 chr16:69478891-69478905 chr16:69478893-69478906 chr16:69478439-69478453 chr16:69478896-69478907
2	IRF1	chr16:69478396-69479003	K562	blood:	n/a	chr16:69478895-69478905 chr16:69478893-69478906 chr16:69478440-69478453 chr16:69478893-69478906 chr16:69478434-69478454 chr16:69478440-69478453 chr16:69478437-69478448 chr16:69478889-69478910 chr16:69478892-69478906 chr16:69478895-69478906 chr16:69478894-69478911 chr16:69478438-69478452 chr16:69478891-69478905 chr16:69478893-69478906 chr16:69478439-69478453 chr16:69478896-69478907
3	PRDM1	chr16:69478491-69479243	Hela-S3	cervix:	n/a	chr16:69478898-69478907 chr16:69478894-69478908 chr16:69478858-69478873 chr16:69478508-69478517 chr16:69478893-69478908 chr16:69478504-69478518 chr16:69478894-69478907
4	GATA1	chr16:69477853-69478870	PBDE	blood:	n/a	chr16:69478644-69478661
5	POLR2A	chr16:69477861-69478533	PBDE	blood:	n/a	n/a
6	STAT3	chr16:69478521-69479023	MCF10A-Er-Src	breast:	n/a	chr16:69478946-69478957 chr16:69478895-69478906
7	IRF1	chr16:69477975-69479335	K562	blood:	n/a	chr16:69478895-69478905 chr16:69478893-69478906 chr16:69478440-69478453 chr16:69478893-69478906 chr16:69478434-69478454 chr16:69478440-69478453 chr16:69478437-69478448 chr16:69478889-69478910 chr16:69478892-69478906 chr16:69478142-69478156 chr16:69478895-69478906 chr16:69478894-69478911 chr16:69478438-69478452 chr16:69478891-69478905 chr16:69478893-69478906 chr16:69478439-69478453 chr16:69478896-69478907
8	JUND	chr16:69478443-69478596	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69418375..69420920-chr16:69477023..69479909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261527	TF binding region
ENSG00000132604	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048086	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs11075720	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs153058	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs246132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs246140	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs246144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246145	0.84[CEU][hapmap]
rs246148	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4783708	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499227	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7185800	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7206737	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728546	0.85[CEU][hapmap]
rs8064195	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs246138	LCAT	cis	parietal	SCAN
rs246138	ZNF23	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69459400-69500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:69459600-69499000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:69459800-69478800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:69466000-69481000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:69466200-69480800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:69466200-69482600	Weak transcription	Brain Germinal Matrix	brain
7	chr16:69466200-69496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:69467000-69486000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:69467000-69486200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:69467800-69480600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr16:69467800-69480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr16:69468000-69480600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:69468000-69482000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:69468200-69480600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:69468200-69480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr16:69468200-69480600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr16:69469400-69484000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr16:69470400-69482400	Weak transcription	Fetal Brain Female	brain
19	chr16:69470600-69492400	Weak transcription	Fetal Intestine Large	intestine
20	chr16:69472600-69480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:69473400-69501600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:69473800-69499600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:69474800-69480600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:69474800-69482600	Weak transcription	Fetal Brain Male	brain
25	chr16:69475000-69479200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr16:69477000-69478600	Genic enhancers	Dnd41	blood
27	chr16:69477000-69478800	Enhancers	HUVEC	blood vessel
28	chr16:69477000-69479200	Genic enhancers	HepG2	liver
29	chr16:69477200-69478800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr16:69477200-69479200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr16:69477800-69478600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr16:69477800-69478600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:69477800-69478600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr16:69477800-69478600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr16:69477800-69478600	Enhancers	Fetal Kidney	kidney
36	chr16:69477800-69478600	Enhancers	NH-A	brain
37	chr16:69477800-69478800	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr16:69477800-69479000	Weak transcription	Fetal Intestine Small	intestine
39	chr16:69477800-69479000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr16:69477800-69479200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr16:69477800-69479200	Enhancers	Fetal Heart	heart
42	chr16:69477800-69479400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr16:69478000-69478600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr16:69478000-69478600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr16:69478000-69478600	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr16:69478000-69478600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr16:69478000-69478600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr16:69478000-69478600	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr16:69478000-69478600	Flanking Active TSS	A549	lung
50	chr16:69478000-69478600	Flanking Active TSS	NHEK	skin

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