Variant report

Variant	rs2114477
Chromosome Location	chr15:42227441-42227442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42219188..42222413-chr15:42224091..42227939,3	MCF-7	breast:
2	chr15:42226413..42228949-chr15:42234016..42236792,3	K562	blood:
3	chr15:42225338..42227544-chr15:42230666..42232718,2	K562	blood:
4	chr15:42217839..42220523-chr15:42226005..42227853,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11070354	0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11631075	0.92[ASW][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634233	0.89[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11638621	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1426889	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1426890	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1648856	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1648857	0.84[ASW][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17687976	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17739125	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2665213	0.92[ASW][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28660334	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4924589	0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493013	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493015	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
5	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
6	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2114477	LCMT2	cis	cerebellum	SCAN
rs2114477	SNAP23	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42210800-42230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:42220800-42230000	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr15:42221200-42228600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:42221600-42229400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:42221600-42232400	Weak transcription	Ovary	ovary
6	chr15:42221800-42230800	Enhancers	Adipose Nuclei	Adipose
7	chr15:42221800-42236400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:42222000-42228000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:42222200-42249800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:42222800-42227800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:42222800-42235200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42222800-42237600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:42223000-42229400	Weak transcription	Psoas Muscle	Psoas
14	chr15:42223000-42236200	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:42223200-42229000	Weak transcription	Brain Anterior Caudate	brain
16	chr15:42223200-42236000	Weak transcription	HepG2	liver
17	chr15:42223200-42243800	Weak transcription	Brain Substantia Nigra	brain
18	chr15:42223400-42229000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:42223400-42229200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:42223600-42229400	Weak transcription	Liver	Liver
21	chr15:42223800-42228600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:42224200-42227600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:42224200-42229400	Genic enhancers	HSMM	muscle
24	chr15:42224400-42227800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr15:42224400-42228000	Enhancers	Right Ventricle	heart
26	chr15:42224400-42228000	Enhancers	NHDF-Ad	bronchial
27	chr15:42224400-42228200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:42224400-42228200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr15:42224400-42228200	Enhancers	Right Atrium	heart
30	chr15:42224400-42229800	Enhancers	Left Ventricle	heart
31	chr15:42224600-42227800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:42224600-42228000	Enhancers	HSMMtube	muscle
33	chr15:42224600-42228200	Enhancers	Esophagus	oesophagus
34	chr15:42224600-42228200	Enhancers	Lung	lung
35	chr15:42224800-42227600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:42224800-42227600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:42224800-42227600	Enhancers	A549	lung
38	chr15:42224800-42228600	Enhancers	HMEC	breast
39	chr15:42224800-42229200	Enhancers	NH-A	brain
40	chr15:42224800-42232600	Enhancers	Fetal Heart	heart
41	chr15:42225000-42228200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr15:42225200-42227600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr15:42225200-42227600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr15:42225200-42229000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:42225200-42230800	Enhancers	Fetal Thymus	thymus
46	chr15:42225400-42227600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:42225400-42227600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr15:42225400-42227600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:42225400-42227800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:42225400-42228200	Enhancers	Pancreas	Pancrea

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