Variant report

Variant	rs4077581
Chromosome Location	chr15:74665514-74665515
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74665429..74667664-chr15:74747982..74750255,2	MCF-7	breast:
2	chr15:74665025..74668014-chr15:74668385..74670407,3	MCF-7	breast:
3	chr15:74664518..74667093-chr15:74731124..74732993,2	MCF-7	breast:
4	chr15:74664221..74666874-chr15:74684631..74687435,2	K562	blood:
5	chr15:74665092..74667430-chr15:74726842..74729796,2	K562	blood:
6	chr15:74664672..74667592-chr15:74837544..74840546,3	MCF-7	breast:
7	chr15:74665365..74667927-chr15:74780037..74785377,6	MCF-7	breast:
8	chr15:74665357..74666676-chr15:74923962..74924983,9	K562	blood:
9	chr15:74664841..74669022-chr15:74717731..74721779,3	K562	blood:
10	chr15:74664899..74666898-chr15:74740722..74743644,2	K562	blood:
11	chr15:74665425..74667643-chr15:74752949..74754890,2	K562	blood:
12	chr15:74664422..74666409-chr15:74928814..74930536,2	MCF-7	breast:
13	chr15:74665122..74667877-chr15:74906569..74911881,5	MCF-7	breast:
14	chr15:74665248..74670570-chr15:74911003..74915113,6	MCF-7	breast:
15	chr15:74665453..74667821-chr15:74780445..74783665,3	MCF-7	breast:
16	chr15:74665280..74666364-chr15:74674391..74675333,6	K562	blood:
17	chr15:74664932..74669170-chr15:74905600..74910371,8	K562	blood:
18	chr15:74665255..74670127-chr15:74905870..74910808,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000260103	Chromatin interaction
ENSG00000247240	Chromatin interaction
ENSG00000212279	Chromatin interaction
ENSG00000261775	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11072478	0.88[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11072479	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438594	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs12440952	0.80[CEU][hapmap]
rs12913682	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914852	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916123	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12916765	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484216	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs1564782	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1843090	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1843091	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2277601	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs2277602	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277605	0.89[EUR][1000 genomes]
rs2277606	0.93[EUR][1000 genomes]
rs2279356	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2279357	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2415239	0.84[EUR][1000 genomes]
rs2930300	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2930301	0.82[EUR][1000 genomes]
rs2930302	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2930304	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930305	0.84[EUR][1000 genomes]
rs2930306	0.96[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2959002	0.85[EUR][1000 genomes]
rs2959004	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959005	0.80[EUR][1000 genomes]
rs2959006	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2959007	0.88[CEU][hapmap]
rs2959008	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2959011	0.80[CEU][hapmap]
rs3825944	0.80[LWK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs4077582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077583	0.86[AFR][1000 genomes]
rs4077584	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs4077585	0.86[AFR][1000 genomes]
rs4598865	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs60636222	0.86[AFR][1000 genomes]
rs6495096	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs68021814	0.82[EUR][1000 genomes]
rs7173655	0.81[EUR][1000 genomes]
rs7174179	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7180275	0.86[AFR][1000 genomes]
rs733434	0.82[EUR][1000 genomes]
rs8031121	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8031424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8039847	0.92[ASN][1000 genomes]
rs900798	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs900799	0.80[CEU][hapmap]
rs900802	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4077581	C15orf39	cis	cerebellum	SCAN
rs4077581	C15orf28	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74658600-74665800	Weak transcription	Pancreas	Pancrea
2	chr15:74658600-74666200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:74658800-74665800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:74658800-74666000	Weak transcription	Esophagus	oesophagus
5	chr15:74658800-74666200	Weak transcription	Right Atrium	heart
6	chr15:74659400-74666200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:74659800-74666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:74660000-74665600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:74660200-74665600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:74660200-74665800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:74660400-74665800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:74661800-74665800	Weak transcription	Fetal Heart	heart
13	chr15:74662000-74665800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr15:74662200-74665800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:74662200-74665800	Weak transcription	Adipose Nuclei	Adipose
16	chr15:74662200-74666200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:74662200-74666200	Weak transcription	Ovary	ovary
18	chr15:74663200-74665800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:74664000-74665600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:74664800-74665600	Weak transcription	Placenta	Placenta
21	chr15:74664800-74665800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:74665400-74665600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:74665400-74665600	Enhancers	Hela-S3	cervix
24	chr15:74665400-74665600	Bivalent Enhancer	HepG2	liver
25	chr15:74665400-74666200	Enhancers	Spleen	Spleen

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