Variant report

Variant	rs12100949
Chromosome Location	chr14:56040787-56040788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56037803..56044083-chr14:56044253..56047931,9	MCF-7	breast:
2	chr14:56039648..56042388-chr14:56046170..56047723,2	MCF-7	breast:
3	chr14:56038401..56042660-chr14:56045839..56048556,3	K562	blood:

Variant related genes	Relation type
ENSG00000126777	Chromatin interaction
ENSG00000186615	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10083303	0.82[AMR][1000 genomes]
rs10083353	0.82[AMR][1000 genomes]
rs10083431	0.85[AMR][1000 genomes]
rs10083493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10083499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs10129890	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129990	0.89[AFR][1000 genomes]
rs10132721	0.91[AFR][1000 genomes]
rs10133962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs10136155	0.82[AMR][1000 genomes]
rs10137340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs10137364	0.85[AMR][1000 genomes]
rs10142497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes]
rs10142757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs10143002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs10146604	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10148983	0.82[AMR][1000 genomes]
rs10149408	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10150498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs10151664	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151733	0.86[AFR][1000 genomes]
rs10483643	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10483645	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10483646	0.87[CEU][hapmap]
rs10483648	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10483650	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12100753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12892022	1.00[CHB][hapmap]
rs12894368	1.00[CHB][hapmap]
rs13379340	0.85[AMR][1000 genomes]
rs13379342	0.82[AMR][1000 genomes]
rs13379343	0.82[AMR][1000 genomes]
rs13379353	0.85[AMR][1000 genomes]
rs17253716	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17253723	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17683614	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17683626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17683656	0.82[AMR][1000 genomes]
rs17683728	0.82[AMR][1000 genomes]
rs17685078	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17685102	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17745459	1.00[CHB][hapmap]
rs17746033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs17746106	0.89[AMR][1000 genomes]
rs17747083	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17747301	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17832365	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2147114	0.82[AMR][1000 genomes]
rs2274075	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2296181	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs28478195	0.89[AMR][1000 genomes]
rs3736876	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs60318423	0.91[AFR][1000 genomes]
rs7150841	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs8007065	0.82[AMR][1000 genomes]
rs8008528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs8008958	0.91[AFR][1000 genomes]
rs8009239	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs8009608	0.82[AMR][1000 genomes]
rs8011213	0.88[AFR][1000 genomes]
rs8019218	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9323289	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9944028	0.82[AMR][1000 genomes]
rs9972177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs9972178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs9972180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12100949	KTN1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12100949	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56023600-56045200	Weak transcription	Primary T cells from cord blood	blood
2	chr14:56024000-56043200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:56024200-56045400	Weak transcription	Adipose Nuclei	Adipose
4	chr14:56024400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr14:56024400-56043600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:56024400-56043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:56024400-56043600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:56024400-56045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:56024400-56045200	Weak transcription	Ovary	ovary
10	chr14:56024400-56045400	Weak transcription	Hela-S3	cervix
11	chr14:56024400-56045400	Weak transcription	Osteobl	bone
12	chr14:56024400-56045800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:56024600-56043800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:56024600-56045400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr14:56025200-56045600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr14:56025800-56045400	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:56026000-56043000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:56026200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:56028000-56044600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr14:56029200-56043600	Weak transcription	HSMM	muscle
21	chr14:56034200-56046000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:56035600-56045800	Weak transcription	Aorta	Aorta
23	chr14:56035800-56043600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr14:56037000-56045600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr14:56037400-56045600	Weak transcription	Fetal Kidney	kidney
26	chr14:56037800-56045600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:56038400-56045200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:56038400-56045200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:56038600-56045000	Weak transcription	HSMMtube	muscle
30	chr14:56038600-56045200	Weak transcription	Brain Substantia Nigra	brain
31	chr14:56039000-56045800	Weak transcription	Primary B cells from cord blood	blood
32	chr14:56039200-56045400	Weak transcription	Right Atrium	heart
33	chr14:56039200-56045400	Weak transcription	HMEC	breast
34	chr14:56039600-56043800	Weak transcription	GM12878-XiMat	blood
35	chr14:56039600-56045000	Weak transcription	Brain Anterior Caudate	brain
36	chr14:56039600-56045200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr14:56039600-56045200	Weak transcription	Fetal Lung	lung
38	chr14:56039600-56045400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:56039600-56045400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr14:56039600-56045400	Weak transcription	Fetal Stomach	stomach
41	chr14:56039600-56045800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:56039800-56041800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr14:56039800-56045000	Weak transcription	Brain Angular Gyrus	brain
44	chr14:56039800-56045000	Weak transcription	Fetal Brain Male	brain
45	chr14:56039800-56045200	Weak transcription	Brain Hippocampus Middle	brain
46	chr14:56039800-56045200	Weak transcription	NH-A	brain
47	chr14:56039800-56045400	Weak transcription	K562	blood
48	chr14:56039800-56045600	Weak transcription	Pancreas	Pancrea
49	chr14:56040000-56045000	Weak transcription	A549	lung
50	chr14:56040000-56045400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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