Variant report

Variant	rs1267308
Chromosome Location	chr1:46987718-46987719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46985914..46991197-chr1:46993744..46997835,5	K562	blood:
2	chr1:46916965..46919039-chr1:46986661..46989583,2	K562	blood:
3	chr1:46985009..46990560-chr1:46990823..46993646,5	K562	blood:
4	chr1:46954395..46956906-chr1:46986850..46988638,2	MCF-7	breast:
5	chr1:46971533..46973952-chr1:46986776..46988731,3	K562	blood:
6	chr1:46986798..46990832-chr1:46991693..46995331,8	K562	blood:
7	chr1:46919084..46921023-chr1:46985929..46988838,3	K562	blood:
8	chr1:46908155..46911848-chr1:46987375..46989663,3	K562	blood:
9	chr1:46908155..46911848-chr1:46987375..46989961,4	K562	blood:
10	chr1:46975501..46977043-chr1:46987288..46989781,2	K562	blood:
11	chr1:46981951..46984222-chr1:46986722..46989512,3	MCF-7	breast:
12	chr1:46950640..46959255-chr1:46986389..46991936,15	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197587	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10890402	0.83[ASN][1000 genomes]
rs11588450	0.80[EUR][1000 genomes]
rs1267301	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267302	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs1267304	0.88[EUR][1000 genomes]
rs1267306	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267309	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs1267310	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1267311	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1267312	0.99[EUR][1000 genomes]
rs1267313	0.99[EUR][1000 genomes]
rs1267314	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1745370	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745371	0.99[EUR][1000 genomes]
rs2404611	0.81[EUR][1000 genomes]
rs2476164	0.99[EUR][1000 genomes]
rs3737740	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57100184	0.80[AMR][1000 genomes]
rs61783087	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6670699	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6696219	0.80[EUR][1000 genomes]
rs7519040	0.99[EUR][1000 genomes]
rs7524253	0.80[EUR][1000 genomes]
rs7542296	0.81[EUR][1000 genomes]
rs942255	0.88[CEU][hapmap];0.90[CHB][hapmap];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	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1267308	KDM4A	cis	parietal	SCAN
rs1267308	MKNK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46983200-46987800	Weak transcription	Pancreas	Pancrea
2	chr1:46983200-46989800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:46984800-46988200	Enhancers	NHEK	skin
4	chr1:46984800-46988600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:46985000-46990200	Enhancers	HMEC	breast
6	chr1:46985200-46987800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:46985600-46988600	Enhancers	HSMMtube	muscle
8	chr1:46985800-46989800	Enhancers	Adipose Nuclei	Adipose
9	chr1:46986000-46988000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:46986400-46987800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:46986400-46987800	Weak transcription	Gastric	stomach
12	chr1:46986400-46987800	Weak transcription	Right Atrium	heart
13	chr1:46986400-46987800	Enhancers	Osteobl	bone
14	chr1:46986400-46988400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:46986400-46988400	Weak transcription	Lung	lung
16	chr1:46986400-46988800	Enhancers	HSMM	muscle
17	chr1:46986600-46987800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:46986600-46987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:46986600-46987800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:46986600-46987800	Weak transcription	Fetal Lung	lung
21	chr1:46986600-46988400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:46986600-46988800	Enhancers	NH-A	brain
23	chr1:46986600-46989000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:46986600-46989000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:46986600-46990000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:46986600-46991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:46986800-46987800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:46986800-46987800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:46986800-46987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:46986800-46987800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:46986800-46987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:46986800-46987800	Enhancers	Hela-S3	cervix
33	chr1:46986800-46987800	Weak transcription	NHLF	lung
34	chr1:46986800-46988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:46986800-46989600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:46987000-46988000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:46987000-46988400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr1:46987000-46988600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
39	chr1:46987000-46988800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr1:46987200-46988800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr1:46987200-46989000	Enhancers	GM12878-XiMat	blood
42	chr1:46987200-46989800	Flanking Active TSS	K562	blood
43	chr1:46987200-46990600	Enhancers	Esophagus	oesophagus
44	chr1:46987400-46988800	Enhancers	NHDF-Ad	bronchial
45	chr1:46987400-46990200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:46987600-46988400	Flanking Active TSS	A549	lung
47	chr1:46987600-46988600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:46987600-46988800	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:46987600-46989200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:46987600-46990400	Enhancers	Stomach Mucosa	stomach

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