Variant report

Variant	rs1151038
Chromosome Location	chr12:32433819-32433820
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32431449..32434130-chr12:32435109..32437179,2	K562	blood:
2	chr12:32433812..32435495-chr12:32439244..32441498,2	MCF-7	breast:
3	chr12:32432630..32434925-chr12:32435109..32437002,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1151039	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151045	0.91[ASN][1000 genomes]
rs1239398	0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1239401	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs155201	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161979	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161980	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161981	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs185487	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2129590	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2594000	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs261868	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs261869	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs261870	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs261875	0.82[JPT][hapmap]
rs261877	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2632344	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632359	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2632365	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650125	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650137	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2728704	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2728705	0.86[ASN][1000 genomes]
rs2728800	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2728801	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs326633	0.84[CHD][hapmap]
rs708225	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs708226	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs708227	0.86[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs751720	0.91[ASN][1000 genomes]
rs753296	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs792473	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs792474	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs792861	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792866	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs806784	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs814243	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs901598	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1151038	BICD1	cis	Thyroid	GTEx
rs1151038	SLC37A1	trans	cerebellum	SCAN
rs1151038	TMTC1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32413400-32437600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:32424400-32434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:32424600-32438000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:32425000-32437800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:32426600-32443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:32426800-32436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:32426800-32436600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:32426800-32437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:32426800-32437400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:32426800-32442800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:32426800-32443200	Weak transcription	NH-A	brain
12	chr12:32426800-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:32427000-32436200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:32427000-32436200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:32427000-32437800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:32427000-32438000	Weak transcription	Fetal Brain Female	brain
17	chr12:32427000-32443400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:32427000-32458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:32427000-32459400	Weak transcription	Aorta	Aorta
20	chr12:32427000-32463000	Weak transcription	NHLF	lung
21	chr12:32427200-32435400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:32427200-32436200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:32427200-32463000	Weak transcription	Fetal Intestine Small	intestine
24	chr12:32427400-32437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:32427400-32445200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:32427600-32454400	Weak transcription	Primary B cells from cord blood	blood
27	chr12:32427800-32436200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:32427800-32438200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:32429000-32436200	Weak transcription	Ovary	ovary
30	chr12:32429400-32437200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:32433200-32436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:32433600-32434400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:32433600-32434400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:32433600-32434800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:32433600-32434800	Enhancers	Fetal Intestine Large	intestine

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