Variant report

Variant	rs2279378
Chromosome Location	chr15:74596494-74596495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ISLR-1	chr15:74596393-74596684	ENSG00000261384.1
2	lnc-ISLR-1	chr15:74596393-74596820	NONHSAT047223

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072478	0.88[MEX][hapmap]
rs11631552	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634685	0.86[ASW][hapmap];0.92[CEU][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11635550	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11856695	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905100	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906092	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913522	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12917295	0.82[CEU][hapmap]
rs1484210	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1809500	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277602	0.80[MEX][hapmap]
rs2899825	0.94[CHB][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs2930291	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2930302	0.88[MEX][hapmap]
rs2959004	0.80[MEX][hapmap]
rs2959008	0.88[MEX][hapmap]
rs2959011	0.96[MEX][hapmap]
rs351184	0.92[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs351189	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs413150	0.90[EUR][1000 genomes]
rs4887131	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4887132	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4887134	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs900799	0.81[CEU][hapmap]
rs900800	0.84[CEU][hapmap]
rs900801	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279378	SEMA7A	cis	cerebellum	SCAN
rs2279378	RPLP1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74584200-74607400	Weak transcription	Right Atrium	heart
2	chr15:74591600-74597400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr15:74592400-74596600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:74592400-74596800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:74592800-74597000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
6	chr15:74592800-74597000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr15:74592800-74597000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr15:74593800-74601000	Enhancers	Fetal Brain Female	brain
9	chr15:74593800-74601800	Enhancers	Fetal Brain Male	brain
10	chr15:74594000-74597200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:74594000-74597800	Enhancers	Brain Germinal Matrix	brain
12	chr15:74594000-74602000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:74594200-74596600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:74594400-74597200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:74594400-74598000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:74594600-74596600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:74594600-74596600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:74594600-74597200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr15:74594600-74597200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr15:74594600-74597200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr15:74594800-74596600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:74595000-74597200	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr15:74595400-74596600	Bivalent Enhancer	Fetal Stomach	stomach
24	chr15:74595400-74596800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr15:74595400-74597200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:74595400-74597200	Enhancers	Spleen	Spleen
27	chr15:74595800-74596600	Enhancers	Fetal Kidney	kidney
28	chr15:74595800-74597200	Bivalent Enhancer	Fetal Lung	lung
29	chr15:74596000-74597800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:74596200-74596600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr15:74596200-74596800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:74596400-74596600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr15:74596400-74596600	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr15:74596400-74596600	Enhancers	A549	lung

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