Variant report

Variant	rs17124448
Chromosome Location	chr12:50514478-50514479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50506976..50509315-chr12:50512886..50514757,3	K562	blood:
2	chr12:50510353..50512301-chr12:50513057..50515415,2	K562	blood:
3	chr12:50513121..50517277-chr12:50517671..50521204,4	MCF-7	breast:
4	chr12:50513117..50516095-chr12:50518308..50520675,3	K562	blood:
5	chr12:50504895..50507498-chr12:50512482..50515401,3	MCF-7	breast:
6	chr12:50506326..50509315-chr12:50512899..50514726,2	K562	blood:
7	chr12:50510457..50512619-chr12:50512712..50515354,2	MCF-7	breast:
8	chr12:50512748..50515503-chr12:50523146..50524991,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10735822	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10735823	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747571	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783334	0.87[EUR][1000 genomes]
rs10783336	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783337	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs10783339	0.84[EUR][1000 genomes]
rs10783341	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs10875999	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876001	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876002	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876007	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169275	0.86[EUR][1000 genomes]
rs11169283	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169284	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169285	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12229758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314572	0.81[ASN][1000 genomes]
rs1862044	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2008537	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2242507	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782323	0.92[GIH][hapmap]
rs55639096	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56151073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131794	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139363	0.92[GIH][hapmap]
rs7297864	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7300549	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7305558	0.92[GIH][hapmap]
rs7306213	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316344	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486874	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7953174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	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
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17124448	SMARCD1	cis	cerebellum	SCAN
rs17124448	MCRS1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50506800-50521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50506800-50523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
4	chr12:50507000-50520800	Weak transcription	NH-A	brain
5	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
11	chr12:50507200-50515400	Weak transcription	Fetal Brain Male	brain
12	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
13	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
14	chr12:50507200-50520800	Weak transcription	NHLF	lung
15	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
18	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:50507400-50514600	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr12:50508400-50518200	Strong transcription	Fetal Stomach	stomach
21	chr12:50508600-50518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:50508600-50518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:50508800-50518000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:50509200-50518200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:50509200-50518400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:50509400-50518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:50509400-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:50509400-50518400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:50509400-50519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:50510000-50517800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:50510000-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:50510400-50515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
36	chr12:50510800-50528400	Strong transcription	Liver	Liver
37	chr12:50511200-50519000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:50511400-50518000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:50511400-50518200	Strong transcription	Lung	lung
41	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:50512000-50518400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:50512200-50519400	Weak transcription	Fetal Heart	heart
44	chr12:50512600-50515400	Strong transcription	K562	blood
45	chr12:50512600-50519000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:50512600-50519200	Strong transcription	Adipose Nuclei	Adipose
47	chr12:50512600-50522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
50	chr12:50512800-50514800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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