Variant report

Variant	rs7959328
Chromosome Location	chr12:10514066-10514067
allele	C/T
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	KAP1	chr12:10513409-10514740	HEK293	kidney:	n/a	n/a
2	POLR2A	chr12:10513493-10514135	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr12:10513497-10514511	K562	blood:	n/a	chr12:10513924-10513934
4	MAX	chr12:10513539-10514145	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
5	E2F6	chr12:10513300-10514304	H1-hESC	embryonic stem cell:	n/a	n/a
6	KAP1	chr12:10513525-10514708	U2OS	brain:	n/a	n/a
7	MYC	chr12:10513648-10514122	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
8	YY1	chr12:10513758-10514080	NT2-D1	testis:	n/a	chr12:10513910-10513922
9	MAX	chr12:10513538-10514114	NB4	blood:	n/a	chr12:10513924-10513934
10	MAX	chr12:10513332-10514456	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
11	MYC	chr12:10513655-10514089	MCF10A-Er-Src	breast:	n/a	chr12:10513924-10513934
12	MYC	chr12:10513540-10514407	MCF10A-Er-Src	breast:	n/a	chr12:10513924-10513934
13	YY1	chr12:10513680-10514104	H1-hESC	embryonic stem cell:	n/a	chr12:10513910-10513922
14	TAF1	chr12:10513727-10514099	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:10513232-10514581	SK-N-MC	brain:	n/a	n/a
16	E2F6	chr12:10513684-10514089	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr12:10513773-10514112	ECC-1	luminal epithelium:	n/a	chr12:10513910-10513922
18	TCF7L2	chr12:10513852-10514704	HEK293	kidney:	n/a	n/a
19	MAX	chr12:10513559-10514550	H1-hESC	embryonic stem cell:	n/a	chr12:10513924-10513934
20	MYC	chr12:10513557-10514115	NB4	blood:	n/a	chr12:10513924-10513934
21	POLR2A	chr12:10513419-10514130	SK-N-MC	brain:	n/a	n/a
22	YY1	chr12:10513667-10514203	H1-hESC	embryonic stem cell:	n/a	chr12:10513910-10513922
23	POLR2A	chr12:10513567-10514107	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000245648	TF binding region
ENSG00000256155	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10743886	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10743887	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772262	0.93[AMR][1000 genomes]
rs10772267	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10845115	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10845117	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4764430	0.82[ASN][1000 genomes]
rs6416265	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6488285	0.82[ASN][1000 genomes]
rs7139147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310643	0.82[ASN][1000 genomes]
rs7486507	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7956385	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970474	0.93[AMR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7959328	KLRK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

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	chr12:10511600-10516400	Weak transcription	Gastric	stomach
4	chr12:10511800-10516200	Weak transcription	Thymus	Thymus
5	chr12:10512200-10515200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:10512800-10515000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:10512800-10515200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr12:10513000-10514200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:10513000-10514800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:10513000-10515600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:10513000-10516400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:10513400-10514200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:10513400-10514200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr12:10513400-10514200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:10513400-10514200	Active TSS	Brain Anterior Caudate	brain
16	chr12:10513400-10514200	Enhancers	Hela-S3	cervix
17	chr12:10513400-10514400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:10513400-10514600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:10513400-10514800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:10513400-10515400	Enhancers	HMEC	breast
21	chr12:10513400-10516200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr12:10513400-10517000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:10513600-10514200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:10513600-10514400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:10513600-10514400	Weak transcription	Primary T cells from cord blood	blood
26	chr12:10513600-10514400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:10513600-10514600	Enhancers	Dnd41	blood
28	chr12:10513600-10515200	Enhancers	Fetal Kidney	kidney
29	chr12:10513600-10516200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:10513600-10516400	Enhancers	Fetal Lung	lung
31	chr12:10513600-10516400	Enhancers	Osteobl	bone
32	chr12:10513600-10516600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:10513600-10516600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:10513600-10516600	Weak transcription	Aorta	Aorta
35	chr12:10513800-10514200	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:10513800-10514400	Active TSS	Brain Cingulate Gyrus	brain
37	chr12:10513800-10514400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr12:10513800-10514400	Enhancers	NH-A	brain
39	chr12:10513800-10514600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:10513800-10514800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:10513800-10515400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:10513800-10515600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:10514000-10514200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr12:10514000-10514200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:10514000-10514200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:10514000-10514200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr12:10514000-10514200	Enhancers	Brain Substantia Nigra	brain
48	chr12:10514000-10514400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr12:10514000-10514400	Enhancers	NHEK	skin
50	chr12:10514000-10514600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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