Variant report

Variant	rs3850967
Chromosome Location	chr12:31726501-31726502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31725804..31727316-chr12:31729688..31732236,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs12809140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812075	0.81[CEU][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12816170	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12816386	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12818749	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12819062	0.84[EUR][1000 genomes]
rs12820294	0.81[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12821808	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12822601	0.87[EUR][1000 genomes]
rs12825207	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12826193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12831480	0.83[EUR][1000 genomes]
rs16918738	0.92[ASN][1000 genomes]
rs16918744	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16918795	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs17497517	0.81[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497656	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497998	0.81[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2126897	0.81[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2271983	1.00[CHB][hapmap]
rs34007930	0.83[EUR][1000 genomes]
rs34094545	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34184789	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34271764	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34308937	0.84[EUR][1000 genomes]
rs34450466	0.92[EUR][1000 genomes]
rs34585237	0.88[EUR][1000 genomes]
rs34642866	0.83[EUR][1000 genomes]
rs34667511	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949976	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34955459	0.84[EUR][1000 genomes]
rs34986122	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35029695	0.86[EUR][1000 genomes]
rs35193529	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35545963	0.90[EUR][1000 genomes]
rs35567364	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35679974	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35692484	0.86[EUR][1000 genomes]
rs35981245	0.85[AFR][1000 genomes]
rs4338625	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4421825	1.00[CHB][hapmap]
rs4930977	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4930981	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930983	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931498	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs4931503	0.81[CEU][hapmap];0.91[MEX][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4931504	0.81[CEU][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4931510	0.81[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931518	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55635343	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55643034	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55771933	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56183451	0.83[EUR][1000 genomes]
rs56234529	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56282720	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56409505	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66479670	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66520413	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs66552209	0.85[EUR][1000 genomes]
rs66597773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66635949	0.90[EUR][1000 genomes]
rs67415228	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67963293	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs68030436	0.81[EUR][1000 genomes]
rs71455664	0.85[EUR][1000 genomes]
rs71455667	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71455668	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71455669	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71455670	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71455671	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73080503	0.86[EUR][1000 genomes]
rs73084486	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086471	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088505	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088597	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv52934	chr12:31721932-31731107	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3850967	BICD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31709200-31727600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:31711000-31727400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:31714200-31728600	Weak transcription	Psoas Muscle	Psoas
4	chr12:31719000-31731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31720000-31727600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:31720000-31731400	Weak transcription	Brain Germinal Matrix	brain
7	chr12:31720200-31727400	Weak transcription	Brain Anterior Caudate	brain
8	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
9	chr12:31722000-31726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:31722200-31731000	Weak transcription	HSMM	muscle
11	chr12:31722800-31727600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:31722800-31727600	Weak transcription	Adipose Nuclei	Adipose
13	chr12:31722800-31727800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:31722800-31730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:31722800-31735200	Weak transcription	Spleen	Spleen
16	chr12:31723600-31728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:31723800-31731400	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:31724000-31726600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:31724000-31727600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:31724000-31728000	Weak transcription	Stomach Mucosa	stomach
21	chr12:31724000-31730800	Weak transcription	HSMMtube	muscle
22	chr12:31724200-31726600	Enhancers	Liver	Liver
23	chr12:31724200-31726600	Weak transcription	Left Ventricle	heart
24	chr12:31724200-31727200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:31724200-31727400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:31724200-31727400	Weak transcription	HUVEC	blood vessel
27	chr12:31724200-31727600	Weak transcription	Brain Substantia Nigra	brain
28	chr12:31724200-31727800	Weak transcription	Fetal Lung	lung
29	chr12:31724200-31727800	Weak transcription	NHLF	lung
30	chr12:31724200-31727800	Weak transcription	Osteobl	bone
31	chr12:31724200-31728600	Weak transcription	Fetal Intestine Small	intestine
32	chr12:31724200-31730800	Weak transcription	Pancreas	Pancrea
33	chr12:31724200-31730800	Weak transcription	Right Atrium	heart
34	chr12:31724200-31731000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:31724200-31731200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:31724200-31731400	Weak transcription	Fetal Kidney	kidney
37	chr12:31724200-31731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:31724400-31726800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:31724400-31728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:31724600-31727600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:31724800-31726600	Weak transcription	Right Ventricle	heart
42	chr12:31725000-31726600	Weak transcription	Ovary	ovary
43	chr12:31725000-31728600	Enhancers	Fetal Heart	heart
44	chr12:31725200-31727000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:31725200-31728200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:31725400-31726600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:31725400-31727000	Enhancers	HepG2	liver
48	chr12:31725600-31728400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:31725800-31726800	Enhancers	Brain Angular Gyrus	brain
50	chr12:31725800-31727200	Enhancers	Cortex derived primary cultured neurospheres	brain

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