Variant report

Variant	rs7178833
Chromosome Location	chr15:57309312-57309313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57209175..57210784-chr15:57308733..57311658,2	K562	blood:
2	chr15:57209364..57212331-chr15:57308276..57309947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10467927	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs10467928	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10467929	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10851612	0.87[CHB][hapmap]
rs11071303	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11071308	0.83[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap]
rs1115019	0.83[CHB][hapmap]
rs11856210	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11856411	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12324092	0.83[TSI][hapmap]
rs13379847	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs1430820	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1430822	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441236	0.83[CHB][hapmap]
rs1657922	0.83[CHB][hapmap]
rs16977153	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16977222	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16977243	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs16977270	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs16977278	0.83[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs17415731	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2169467	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2278613	0.87[CHB][hapmap]
rs2464429	0.85[YRI][hapmap]
rs2464430	0.86[YRI][hapmap]
rs2470079	0.82[YRI][hapmap]
rs2470082	0.83[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]
rs2593211	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2593249	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2593252	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2703576	0.89[YRI][hapmap]
rs2703614	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs2733188	0.89[YRI][hapmap]
rs2733333	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2733334	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs28360967	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28422021	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28505122	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28533433	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28541606	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28612876	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28648577	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28649108	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28654848	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28677775	0.89[ASN][1000 genomes]
rs28712697	0.80[AMR][1000 genomes]
rs28756149	0.86[ASN][1000 genomes]
rs2920267	0.88[YRI][hapmap]
rs2951899	0.89[MKK][hapmap];0.88[YRI][hapmap]
rs2951903	0.89[YRI][hapmap]
rs2951904	0.81[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap]
rs2962991	0.85[YRI][hapmap]
rs2962992	0.85[LWK][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs4774245	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6493900	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6493902	0.89[YRI][hapmap]
rs7162194	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163267	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs7164655	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs7169053	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7171073	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7171304	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7175191	0.87[CHB][hapmap]
rs7175436	0.82[YRI][hapmap]
rs7176873	0.88[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8023343	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8023816	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026702	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs8031516	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8031640	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032615	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033010	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034066	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8034502	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs8035485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8035916	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs8039899	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040708	0.80[EUR][1000 genomes]
rs9302200	0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs9806170	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs9806199	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]

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	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
2	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
3	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7178833	RAB27A	cis	cerebellum	SCAN
rs7178833	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7178833	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:57282200-57311000	Weak transcription	K562	blood
5	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:57286200-57312000	Weak transcription	HSMM	muscle
8	chr15:57286200-57314800	Weak transcription	Dnd41	blood
9	chr15:57286400-57309400	Weak transcription	Fetal Lung	lung
10	chr15:57289600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:57289600-57315600	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:57289800-57315600	Weak transcription	Primary B cells from cord blood	blood
13	chr15:57294400-57311600	Weak transcription	GM12878-XiMat	blood
14	chr15:57295200-57313600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:57296400-57309400	Weak transcription	NHDF-Ad	bronchial
16	chr15:57296400-57310200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:57296600-57313200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:57297200-57316800	Weak transcription	Fetal Stomach	stomach
19	chr15:57299200-57316000	Weak transcription	Right Ventricle	heart
20	chr15:57299200-57317200	Weak transcription	Esophagus	oesophagus
21	chr15:57300200-57313800	Strong transcription	Fetal Thymus	thymus
22	chr15:57303600-57317600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:57305000-57310800	Weak transcription	Spleen	Spleen
24	chr15:57305000-57311200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:57305000-57311800	Weak transcription	Aorta	Aorta
26	chr15:57305000-57312000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:57305000-57313400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:57305000-57313400	Weak transcription	Right Atrium	heart
29	chr15:57306400-57310600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:57306400-57310600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:57306400-57312400	Enhancers	Placenta	Placenta
32	chr15:57307000-57311600	Weak transcription	NHLF	lung
33	chr15:57307400-57309400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:57307400-57309400	Enhancers	Colon Smooth Muscle	Colon
35	chr15:57307400-57309400	Enhancers	NHEK	skin
36	chr15:57307400-57309600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:57307400-57309800	Enhancers	HMEC	breast
38	chr15:57307400-57311000	Enhancers	Fetal Intestine Large	intestine
39	chr15:57307600-57309400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr15:57307600-57309400	Enhancers	Liver	Liver
41	chr15:57307600-57309600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:57307600-57309800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:57307600-57312200	Enhancers	Brain Anterior Caudate	brain
44	chr15:57307600-57312400	Enhancers	A549	lung
45	chr15:57307600-57312800	Enhancers	Brain Substantia Nigra	brain
46	chr15:57307800-57309400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr15:57307800-57309600	Enhancers	Stomach Mucosa	stomach
48	chr15:57307800-57310000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:57307800-57312600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:57307800-57313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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