Variant report

Variant	rs7967954
Chromosome Location	chr12:50673484-50673485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50665714..50669767-chr12:50671688..50676181,4	MCF-7	breast:
2	chr12:50640226..50641774-chr12:50672197..50675094,2	K562	blood:
3	chr12:50672633..50674582-chr12:50677546..50679089,2	K562	blood:
4	chr12:50672480..50674370-chr12:50677048..50678907,2	MCF-7	breast:
5	chr12:50666860..50670693-chr12:50671075..50676885,6	K562	blood:
6	chr12:50671138..50674964-chr12:50675618..50679032,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203433	Chromatin interaction
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10219559	0.85[AMR][1000 genomes]
rs1044370	0.90[ASW][hapmap];0.87[LWK][hapmap];0.83[YRI][hapmap]
rs10747573	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10783342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783343	0.84[AMR][1000 genomes]
rs1362984	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1862042	0.81[AMR][1000 genomes]
rs2004283	0.84[AMR][1000 genomes]
rs2160994	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs2358538	0.89[ASW][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs4459386	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580729	0.90[ASW][hapmap];0.87[LWK][hapmap];0.91[YRI][hapmap]
rs6580732	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580734	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6580738	0.94[LWK][hapmap];0.81[MKK][hapmap]
rs7136648	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7308356	0.91[YRI][hapmap]
rs7308692	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7309519	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9668955	0.82[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7967954	NELL2	cis	cerebellum	SCAN
rs7967954	LASS5	cis	multi-tissue	Pritchard
rs7967954	DIP2B	cis	cerebellum	SCAN
rs7967954	LASS5	cis	parietal	SCAN
rs7967954	CERS5	cis	Nerve Tibial	GTEx
rs7967954	LASS5	cis	cerebellum	SCAN
rs7967954	MCRS1	cis	parietal	SCAN
rs7967954	SLC4A8	cis	parietal	SCAN
rs7967954	SMARCD1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50652200-50675800	Weak transcription	Fetal Stomach	stomach
2	chr12:50652400-50676200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:50652400-50676400	Weak transcription	HSMM	muscle
4	chr12:50662200-50676400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:50665000-50676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50665600-50675800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:50665600-50676200	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:50665800-50676000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:50665800-50676400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:50666000-50674800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:50666000-50675200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:50666000-50676400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:50666000-50676400	Weak transcription	Ovary	ovary
14	chr12:50666200-50675600	Weak transcription	Fetal Lung	lung
15	chr12:50666200-50676400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:50666200-50676400	Weak transcription	Liver	Liver
17	chr12:50666400-50676400	Weak transcription	Right Ventricle	heart
18	chr12:50667600-50674600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:50668200-50676200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:50668600-50676400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:50669800-50675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:50669800-50676400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:50669800-50676400	Weak transcription	HMEC	breast
24	chr12:50670000-50676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:50670200-50675800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:50670200-50676200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:50670200-50676200	Weak transcription	Pancreas	Pancrea
28	chr12:50670200-50676400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:50670200-50676400	Weak transcription	NHEK	skin
30	chr12:50670400-50675400	Weak transcription	Adipose Nuclei	Adipose
31	chr12:50670600-50676400	Weak transcription	Lung	lung
32	chr12:50671000-50676200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:50671000-50676400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:50671400-50675200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:50671400-50676200	Weak transcription	Osteobl	bone
36	chr12:50671400-50676400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:50671400-50676400	Weak transcription	K562	blood
38	chr12:50671600-50674400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:50671600-50674600	Weak transcription	HepG2	liver
40	chr12:50671600-50675000	Weak transcription	Colonic Mucosa	Colon
41	chr12:50671600-50675000	Weak transcription	Stomach Mucosa	stomach
42	chr12:50671600-50675200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:50671600-50675400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50671600-50675400	Weak transcription	NHDF-Ad	bronchial
45	chr12:50671600-50675600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:50671600-50676200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:50671600-50676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:50671600-50676400	Weak transcription	Psoas Muscle	Psoas
49	chr12:50671600-50676400	Weak transcription	A549	lung
50	chr12:50671800-50675400	Weak transcription	Small Intestine	intestine

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