Variant report

Variant	rs325425
Chromosome Location	chr12:32531212-32531213
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32530472..32534353-chr12:32830607..32833580,3	K562	blood:

Variant related genes	Relation type
ENSG00000087470	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10771942	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10771943	0.94[JPT][hapmap]
rs11051951	0.84[JPT][hapmap]
rs11051960	0.92[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12580872	0.81[JPT][hapmap]
rs1471909	0.84[CEU][hapmap]
rs155202	0.81[CEU][hapmap]
rs2062600	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2270787	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs2388987	0.84[CEU][hapmap]
rs2651377	0.96[CEU][hapmap]
rs2728678	0.85[JPT][hapmap]
rs2931550	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325416	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs325418	1.00[CEU][hapmap]
rs325426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325427	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs325428	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs325436	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs325437	0.92[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4444169	0.82[EUR][1000 genomes]
rs7298319	0.92[CEU][hapmap]
rs7298381	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs7484762	0.81[CEU][hapmap]
rs7958506	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959002	0.80[CEU][hapmap]

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	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	nsv438201	chr12:32523455-32531212	Weak transcription Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv526183	chr12:32531212-32535815	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs325425	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32475600-32532400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:32492400-32532000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:32494200-32533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:32518800-32531800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:32519200-32532000	Weak transcription	NHDF-Ad	bronchial
6	chr12:32520800-32532400	Weak transcription	Fetal Intestine Small	intestine
7	chr12:32522400-32532200	Weak transcription	Osteobl	bone
8	chr12:32522600-32535800	Weak transcription	Fetal Brain Female	brain
9	chr12:32522800-32532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:32529800-32532000	Weak transcription	Ovary	ovary
11	chr12:32530600-32532000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:32530600-32532400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:32530600-32534000	Weak transcription	HSMM	muscle
14	chr12:32530800-32531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:32530800-32531800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:32530800-32531800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:32530800-32532000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:32530800-32532000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:32530800-32532000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:32530800-32532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:32530800-32532200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:32530800-32532200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:32531000-32532000	Weak transcription	K562	blood
24	chr12:32531000-32533400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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