Variant report

Variant	rs4774245
Chromosome Location	chr15:57225148-57225149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57222920..57225645-chr15:57236445..57240161,3	MCF-7	breast:
2	chr15:57222937..57225630-chr15:57226421..57228724,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10467927	0.87[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10851612	0.82[CHB][hapmap]
rs1115019	0.87[CHB][hapmap]
rs11856338	0.82[YRI][hapmap]
rs11856411	0.86[CEU][hapmap];0.96[CHB][hapmap];0.90[JPT][hapmap]
rs12440219	0.90[YRI][hapmap]
rs12902058	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs12906025	0.96[YRI][hapmap]
rs13379847	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1430820	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1430822	0.86[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1441236	0.87[CHB][hapmap]
rs1629339	0.80[ASN][1000 genomes]
rs1652747	0.80[ASN][1000 genomes]
rs1657922	0.87[CHB][hapmap]
rs1660958	0.80[ASN][1000 genomes]
rs16977153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977243	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs17415731	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1820994	0.84[AMR][1000 genomes]
rs2111890	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2169467	0.86[CEU][hapmap];0.96[CHB][hapmap];0.85[JPT][hapmap]
rs2278613	0.82[CHB][hapmap]
rs28360967	0.85[ASN][1000 genomes]
rs28612876	0.84[ASN][1000 genomes]
rs28639536	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28648577	0.85[ASN][1000 genomes]
rs28649108	0.86[ASN][1000 genomes]
rs28654848	0.85[ASN][1000 genomes]
rs28677775	0.88[ASN][1000 genomes]
rs28756149	0.87[ASN][1000 genomes]
rs28814080	0.94[ASN][1000 genomes]
rs4774246	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6493900	0.87[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs7162194	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7163267	0.87[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs7164655	0.87[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7168945	0.83[YRI][hapmap]
rs7171073	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7171304	0.90[CEU][hapmap]
rs7175191	0.82[CHB][hapmap]
rs7176873	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7178833	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8023343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023816	0.85[ASN][1000 genomes]
rs8031516	0.83[ASN][1000 genomes]
rs8031640	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs8032615	0.87[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs8034066	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs8035485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039899	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9302200	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs9806170	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs9806199	0.87[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
2	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774245	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57230400	Weak transcription	Lung	lung
2	chr15:57212400-57233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
4	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:57212800-57227200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:57213000-57227400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:57213400-57226800	Weak transcription	Brain Germinal Matrix	brain
9	chr15:57215600-57227400	Weak transcription	Fetal Brain Female	brain
10	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
11	chr15:57220000-57226000	Enhancers	Fetal Intestine Large	intestine
12	chr15:57220200-57226200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr15:57220400-57226800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr15:57220400-57236400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:57220800-57226200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:57221000-57226000	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:57221000-57226600	Enhancers	Fetal Intestine Small	intestine
18	chr15:57221200-57226600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:57221400-57226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:57221400-57227200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:57221600-57226400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr15:57221600-57226600	Weak transcription	HSMMtube	muscle
23	chr15:57221800-57226800	Enhancers	Brain Anterior Caudate	brain
24	chr15:57222000-57225200	Weak transcription	A549	lung
25	chr15:57222000-57225800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:57222200-57225800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr15:57222200-57226000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:57222200-57226200	Weak transcription	NHEK	skin
29	chr15:57222400-57227000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:57222400-57227400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:57222400-57229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:57222400-57231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:57222600-57226600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:57222600-57228800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:57222600-57229000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:57222600-57231200	Weak transcription	Osteobl	bone
37	chr15:57222600-57231800	Weak transcription	HSMM	muscle
38	chr15:57222600-57233000	Weak transcription	Right Ventricle	heart
39	chr15:57222600-57250200	Weak transcription	NH-A	brain
40	chr15:57222800-57231800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:57222800-57232600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:57222800-57240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:57222800-57255000	Weak transcription	HMEC	breast
44	chr15:57223000-57226200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:57223000-57227400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:57223000-57236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:57223200-57226400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:57223200-57226600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:57223200-57226600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:57223200-57227000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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