Variant report

Variant	rs11051950
Chromosome Location	chr12:32502059-32502060
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1058640	0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10771940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844193	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11051960	0.83[EUR][1000 genomes]
rs12827421	0.92[EUR][1000 genomes]
rs155202	0.84[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1809599	0.81[EUR][1000 genomes]
rs2388987	0.81[CEU][hapmap]
rs325416	0.84[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs325428	0.84[CEU][hapmap];0.96[EUR][1000 genomes]
rs325429	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs325431	0.97[EUR][1000 genomes]
rs325432	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325436	0.83[EUR][1000 genomes]
rs325437	0.83[EUR][1000 genomes]
rs4444169	0.82[EUR][1000 genomes]
rs6488045	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6488046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298319	0.81[JPT][hapmap]
rs7314141	0.81[JPT][hapmap]
rs7397498	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7484762	0.84[CEU][hapmap];0.97[EUR][1000 genomes]
rs7959002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964583	0.86[JPT][hapmap]
rs901599	0.82[JPT][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11051950	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32460400-32514600	Weak transcription	HMEC	breast
2	chr12:32475600-32532400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:32475800-32502200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:32475800-32512200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:32476400-32505600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:32476400-32515400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:32479200-32502200	Weak transcription	NHDF-Ad	bronchial
8	chr12:32479200-32504200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:32480600-32524800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:32481400-32511800	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:32484400-32515600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:32485800-32520000	Weak transcription	Fetal Kidney	kidney
13	chr12:32486000-32510800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:32487200-32502400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:32490800-32518600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:32492000-32503800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:32492200-32502600	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:32492200-32505200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:32492200-32514000	Weak transcription	Aorta	Aorta
20	chr12:32492200-32514200	Weak transcription	Lung	lung
21	chr12:32492200-32518600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:32492200-32518600	Weak transcription	Brain Germinal Matrix	brain
23	chr12:32492200-32522000	Weak transcription	Fetal Stomach	stomach
24	chr12:32492200-32523800	Weak transcription	Primary T cells from cord blood	blood
25	chr12:32492200-32523800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:32492200-32527400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:32492200-32530400	Weak transcription	Thymus	Thymus
28	chr12:32492400-32514600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:32492400-32518600	Weak transcription	HSMMtube	muscle
30	chr12:32492400-32522000	Weak transcription	Fetal Brain Female	brain
31	chr12:32492400-32524200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:32492400-32527200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:32492400-32532000	Weak transcription	Brain Angular Gyrus	brain
34	chr12:32492600-32502600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:32492600-32523200	Weak transcription	Primary B cells from cord blood	blood
36	chr12:32493000-32512200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:32493000-32522000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:32493200-32521200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:32493800-32515000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:32493800-32516200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:32493800-32518400	Weak transcription	Osteobl	bone
42	chr12:32494000-32518600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:32494000-32518600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:32494200-32515400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:32494200-32533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:32494400-32514600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:32494800-32515400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:32496800-32504000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:32497400-32502200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:32497400-32508400	Weak transcription	Ovary	ovary

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