Variant report

Variant	rs1271044
Chromosome Location	chr15:83512253-83512254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83512168..83513962-chr15:83673540..83675168,2	MCF-7	breast:
2	chr15:83503713..83505246-chr15:83511567..83513802,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOMER2-1	chr15:83509838-83513971	NONHSAT047869

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11259948	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11259949	0.93[EUR][1000 genomes]
rs11259952	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902970	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12903411	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12907913	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1971555	0.96[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2379996	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2890314	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4260027	0.82[ASW][hapmap]
rs4779068	0.87[JPT][hapmap]
rs4779069	0.86[JPT][hapmap]
rs66851469	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8025432	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8041231	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042254	0.87[MKK][hapmap]

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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats 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	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	esv3443764	chr15:83512166-83512313	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1271044	WHAMM	cis	Adipose Subcutaneous	GTEx
rs1271044	BTBD1	cis	cerebellum	SCAN
rs1271044	WHDC1	cis	multi-tissue	Pritchard
rs1271044	EFTUD1	cis	cerebellum	SCAN
rs1271044	WHAMM	cis	Liver	GTEx
rs1271044	MEX3B	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83500400-83517600	Weak transcription	Fetal Heart	heart
2	chr15:83503600-83514400	Weak transcription	K562	blood
3	chr15:83503600-83518200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:83503600-83518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:83503600-83518600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
7	chr15:83505000-83513600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:83505000-83518200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:83505800-83520800	Weak transcription	Dnd41	blood
10	chr15:83505800-83522400	Weak transcription	Fetal Kidney	kidney
11	chr15:83506000-83514600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:83506000-83518400	Weak transcription	NH-A	brain
13	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:83506200-83512400	Weak transcription	GM12878-XiMat	blood
15	chr15:83506200-83512600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:83506200-83512800	Weak transcription	NHEK	skin
17	chr15:83506200-83513600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:83506200-83513800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:83506200-83518400	Weak transcription	NHDF-Ad	bronchial
20	chr15:83506200-83518800	Weak transcription	Brain Angular Gyrus	brain
21	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:83506400-83518200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:83506400-83518600	Weak transcription	Ovary	ovary
25	chr15:83506400-83518800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:83506600-83512600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:83506600-83512600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr15:83506600-83513600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:83506600-83518200	Weak transcription	Right Ventricle	heart
30	chr15:83506800-83513400	Weak transcription	Fetal Thymus	thymus
31	chr15:83506800-83518200	Weak transcription	A549	lung
32	chr15:83507000-83513400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:83507000-83514600	Weak transcription	Placenta	Placenta
34	chr15:83507000-83515200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:83507000-83517000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:83507000-83518000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:83507000-83518200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:83507000-83518200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:83507000-83518600	Weak transcription	Spleen	Spleen
40	chr15:83507200-83512600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:83507200-83512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:83507200-83512800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:83507200-83512800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:83507200-83518000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:83507200-83518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:83507200-83518200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:83507200-83518200	Weak transcription	Colon Smooth Muscle	Colon
48	chr15:83507200-83518200	Weak transcription	Esophagus	oesophagus
49	chr15:83507200-83518600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine

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