Variant report

Variant	rs2930291
Chromosome Location	chr15:74604834-74604835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74427753..74430311-chr15:74603237..74605329,2	K562	blood:
2	chr15:74604669..74607171-chr17:59473945..59476764,2	MCF-7	breast:
3	chr15:74428468..74430311-chr15:74603033..74605329,2	K562	blood:
4	chr15:74590504..74592017-chr15:74603747..74605953,2	K562	blood:
5	chr15:74604086..74605037-chr15:74614467..74615451,3	K562	blood:
6	chr15:74603389..74605701-chr15:74607624..74611476,3	K562	blood:
7	chr15:74594780..74601167-chr15:74601665..74605713,5	K562	blood:

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000261384	Chromatin interaction
ENSG00000140481	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11072478	0.82[CEU][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes]
rs11631552	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632698	0.84[CEU][hapmap]
rs11634685	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs11635047	0.81[CEU][hapmap]
rs11638442	0.84[CEU][hapmap]
rs11856695	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905100	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906092	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913522	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12917295	0.87[CEU][hapmap]
rs1484210	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1484216	0.81[CEU][hapmap]
rs1564783	0.84[CEU][hapmap]
rs1809500	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277602	0.84[MEX][hapmap]
rs2279378	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]
rs2415239	0.80[EUR][1000 genomes]
rs2899825	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2930300	0.82[CEU][hapmap]
rs2930302	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs2959004	0.84[MEX][hapmap]
rs2959006	0.82[CEU][hapmap]
rs2959007	0.82[CEU][hapmap]
rs2959008	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs2959011	0.83[MEX][hapmap]
rs351184	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs397074	0.83[EUR][1000 genomes]
rs4887131	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4887132	0.86[EUR][1000 genomes]
rs4887134	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4887135	0.84[CEU][hapmap]
rs900799	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs900800	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs900801	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2930291	RPLP1	cis	parietal	SCAN
rs2930291	SEMA7A	cis	cerebellum	SCAN
rs2930291	ITGA11	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74584200-74607400	Weak transcription	Right Atrium	heart
2	chr15:74596600-74606600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:74596600-74609800	Weak transcription	A549	lung
4	chr15:74601200-74607800	Weak transcription	Fetal Lung	lung
5	chr15:74603000-74610800	Enhancers	Fetal Brain Male	brain
6	chr15:74603200-74605200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:74603200-74605600	Enhancers	Brain Germinal Matrix	brain
8	chr15:74603400-74605600	Enhancers	Fetal Brain Female	brain
9	chr15:74603600-74606200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:74603800-74605200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:74603800-74605800	Enhancers	Fetal Muscle Leg	muscle
12	chr15:74604000-74605000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:74604200-74605000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:74604200-74605400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:74604200-74605400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr15:74604200-74607400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:74604200-74613400	Enhancers	Placenta	Placenta
18	chr15:74604400-74605000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:74604400-74605600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:74604400-74605600	Enhancers	Fetal Intestine Small	intestine
21	chr15:74604400-74607000	Weak transcription	NH-A	brain
22	chr15:74604400-74607200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:74604400-74613200	Enhancers	Fetal Thymus	thymus
24	chr15:74604600-74605000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr15:74604600-74606200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:74604600-74607000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:74604600-74607200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:74604600-74607200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:74604600-74607200	Weak transcription	HSMM	muscle
30	chr15:74604600-74608400	Weak transcription	Hela-S3	cervix
31	chr15:74604800-74605200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:74604800-74605200	Enhancers	K562	blood
33	chr15:74604800-74606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:74604800-74606000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:74604800-74606400	Weak transcription	Thymus	Thymus
36	chr15:74604800-74607200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:74604800-74623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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