Variant report

Variant	rs10845121
Chromosome Location	chr12:10513579-10513580
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	SETDB1	chr12:10513268-10513971	U2OS	brain:	n/a	n/a
2	KAP1	chr12:10513409-10514740	HEK293	kidney:	n/a	n/a
3	ZNF263	chr12:10513258-10514065	HEK293-T-REx	kidney:	n/a	chr12:10513644-10513665
4	POLR2A	chr12:10513493-10514135	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr12:10513497-10514511	K562	blood:	n/a	chr12:10513924-10513934
6	MAX	chr12:10513539-10514145	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
7	E2F6	chr12:10513300-10514304	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr12:10513525-10514708	U2OS	brain:	n/a	n/a
9	MYC	chr12:10513532-10514019	K562	blood:	n/a	chr12:10513924-10513934
10	MAX	chr12:10513538-10514114	NB4	blood:	n/a	chr12:10513924-10513934
11	SP1	chr12:10513509-10514019	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr12:10513332-10514456	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
13	MYC	chr12:10513540-10514407	MCF10A-Er-Src	breast:	n/a	chr12:10513924-10513934
14	POLR2A	chr12:10513232-10514581	SK-N-MC	brain:	n/a	n/a
15	TBL1XR1	chr12:10513457-10513639	K562	blood:	n/a	n/a
16	MAX	chr12:10513559-10514550	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
17	MYC	chr12:10513557-10514115	NB4	blood:	n/a	chr12:10513924-10513934
18	POLR2A	chr12:10513419-10514130	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:10513567-10514107	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-277P12.7.1-1	chr12:10513183-10513644	ENSG00000256155

Variant related genes	Relation type
ENSG00000245648	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10734826	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10734827	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10734828	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10772264	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10772268	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10845119	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11053771	1.00[JPT][hapmap]
rs2045882	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2045883	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4764422	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs6488283	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6488284	0.82[AFR][1000 genomes]
rs7960051	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3351751	chr12:10472734-10522269	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
8	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10845121	CLEC4E	cis	parietal	SCAN
rs10845121	PLEKHG6	cis	cerebellum	SCAN
rs10845121	KLRC4	cis	parietal	SCAN
rs10845121	CLEC6A	cis	parietal	SCAN
rs10845121	KLRK1	cis	parietal	SCAN
rs10845121	CLEC1B	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10507400-10515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:10508000-10515200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:10509200-10513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:10509600-10513600	Weak transcription	Fetal Kidney	kidney
5	chr12:10511600-10516400	Weak transcription	Gastric	stomach
6	chr12:10511800-10514000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:10511800-10516200	Weak transcription	Thymus	Thymus
8	chr12:10512200-10514000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:10512200-10515200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:10512800-10515000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:10512800-10515200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr12:10513000-10513800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr12:10513000-10513800	Enhancers	Brain Hippocampus Middle	brain
14	chr12:10513000-10514200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:10513000-10514800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:10513000-10515600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:10513000-10516400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:10513200-10513600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:10513200-10514000	Enhancers	K562	blood
20	chr12:10513400-10513600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:10513400-10513600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr12:10513400-10513600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr12:10513400-10513600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:10513400-10513600	Enhancers	Primary T cells from cord blood	blood
25	chr12:10513400-10513600	Enhancers	Aorta	Aorta
26	chr12:10513400-10513600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr12:10513400-10513800	Enhancers	NHEK	skin
28	chr12:10513400-10514000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:10513400-10514000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:10513400-10514000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:10513400-10514000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:10513400-10514200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:10513400-10514200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:10513400-10514200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:10513400-10514200	Active TSS	Brain Anterior Caudate	brain
36	chr12:10513400-10514200	Enhancers	Hela-S3	cervix
37	chr12:10513400-10514400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr12:10513400-10514600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:10513400-10514800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:10513400-10515400	Enhancers	HMEC	breast
41	chr12:10513400-10516200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr12:10513400-10517000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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