Variant report

Variant	rs1256424
Chromosome Location	chr15:83524257-83524258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83524106..83526544-chr15:83528927..83531403,2	MCF-7	breast:
2	chr15:83522860..83525020-chr15:83654105..83656593,2	MCF-7	breast:
3	chr15:83518647..83521952-chr15:83521961..83525177,3	K562	blood:

Variant related genes	Relation type
ENSG00000169612	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1021022	0.86[EUR][1000 genomes]
rs12385947	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12442119	0.84[LWK][hapmap];0.83[MKK][hapmap]
rs1256426	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256428	0.85[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1256432	0.84[AMR][1000 genomes]
rs1256436	0.82[EUR][1000 genomes]
rs1256438	0.81[EUR][1000 genomes]
rs1256439	0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1256440	0.86[EUR][1000 genomes]
rs1256441	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1256442	0.86[EUR][1000 genomes]
rs1256443	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1256444	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1256445	0.86[EUR][1000 genomes]
rs1256446	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1256447	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1256448	0.81[EUR][1000 genomes]
rs1256449	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1256450	0.86[EUR][1000 genomes]
rs1256454	0.96[CEU][hapmap];0.81[GIH][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12594415	0.85[AFR][1000 genomes]
rs1588546	0.88[JPT][hapmap]
rs17158168	0.88[JPT][hapmap]
rs17158194	0.88[JPT][hapmap]
rs17294229	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2251275	0.94[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2306428	0.82[JPT][hapmap]
rs2621226	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2667376	0.86[ASN][1000 genomes]
rs2667377	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap]
rs2667378	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2667379	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2667380	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2667384	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs3784366	0.88[JPT][hapmap]
rs3784376	0.86[AFR][1000 genomes]
rs3784377	0.82[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs55633961	0.91[AFR][1000 genomes]
rs7173264	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7173683	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7174726	0.88[JPT][hapmap]
rs750234	0.88[ASW][hapmap];0.85[CEU][hapmap];0.90[MKK][hapmap];0.94[YRI][hapmap]
rs8030940	0.88[JPT][hapmap]
rs8036957	0.85[AFR][1000 genomes]
rs880289	0.89[AFR][1000 genomes]
rs899746	0.82[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1256424	TM6SF1	cis	lymphoblastoid	seeQTL
rs1256424	CNR2	trans	cerebellum	SCAN
rs1256424	BTBD1	cis	cerebellum	SCAN
rs1256424	WHAMM	cis	Adipose Subcutaneous	GTEx
rs1256424	RASGRF1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
5	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
7	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
10	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
12	chr15:83519200-83524400	Strong transcription	Gastric	stomach
13	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:83519600-83525600	Weak transcription	HSMMtube	muscle
17	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
18	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:83520000-83524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:83520000-83543600	Weak transcription	HSMM	muscle
21	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
24	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:83521000-83524400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:83521600-83524600	Weak transcription	Osteobl	bone
27	chr15:83521800-83526400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:83521800-83529400	Weak transcription	Primary B cells from cord blood	blood
29	chr15:83522000-83524400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:83522200-83524400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr15:83522200-83524400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:83522400-83524600	Weak transcription	NH-A	brain
33	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:83522600-83529000	Weak transcription	Fetal Kidney	kidney
35	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:83522800-83524400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:83522800-83524600	Weak transcription	Thymus	Thymus
38	chr15:83523000-83524400	Weak transcription	Fetal Thymus	thymus
39	chr15:83523000-83527000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:83523400-83524600	Enhancers	Spleen	Spleen
41	chr15:83523400-83525800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:83523400-83540000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:83523400-83540800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:83523600-83525400	Strong transcription	Pancreas	Pancrea
45	chr15:83523600-83526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:83523600-83541400	Weak transcription	Fetal Stomach	stomach
47	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
48	chr15:83523800-83527400	Weak transcription	Liver	Liver
49	chr15:83523800-83535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:83524000-83525400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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