Variant report

Variant	rs7298319
Chromosome Location	chr12:32530385-32530386
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1045751	0.81[EUR][1000 genomes]
rs1058640	0.81[JPT][hapmap]
rs10771940	0.81[JPT][hapmap]
rs10771941	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771942	0.96[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10844193	0.81[JPT][hapmap]
rs10844194	0.80[AFR][1000 genomes]
rs10844197	0.83[EUR][1000 genomes]
rs10844198	0.82[EUR][1000 genomes]
rs11051950	0.81[JPT][hapmap]
rs11051960	0.92[CEU][hapmap]
rs1128591	0.81[EUR][1000 genomes]
rs1471909	0.84[CEU][hapmap]
rs155202	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs167806	0.81[EUR][1000 genomes]
rs1809601	0.91[ASN][1000 genomes]
rs188978	0.81[EUR][1000 genomes]
rs188979	0.82[EUR][1000 genomes]
rs2270787	0.81[CEU][hapmap]
rs2388987	0.84[CEU][hapmap]
rs2450506	0.80[EUR][1000 genomes]
rs2455004	0.82[EUR][1000 genomes]
rs2632337	0.80[EUR][1000 genomes]
rs2632363	0.81[EUR][1000 genomes]
rs2651366	0.83[EUR][1000 genomes]
rs2651367	0.82[EUR][1000 genomes]
rs2651368	0.83[EUR][1000 genomes]
rs2651377	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2733694	0.83[EUR][1000 genomes]
rs2733696	0.83[EUR][1000 genomes]
rs2733703	0.82[EUR][1000 genomes]
rs2733704	0.82[EUR][1000 genomes]
rs2733705	0.83[EUR][1000 genomes]
rs2931554	0.82[EUR][1000 genomes]
rs325416	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs325418	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs325419	0.81[EUR][1000 genomes]
rs325420	0.82[EUR][1000 genomes]
rs325421	0.81[EUR][1000 genomes]
rs325424	0.82[EUR][1000 genomes]
rs325425	0.92[CEU][hapmap]
rs325426	0.92[CEU][hapmap]
rs325428	0.81[CEU][hapmap]
rs325429	0.81[JPT][hapmap]
rs325436	0.91[CEU][hapmap]
rs325437	0.92[CEU][hapmap]
rs56146365	0.93[EUR][1000 genomes]
rs6488048	0.97[ASN][1000 genomes]
rs6488049	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135763	0.90[ASN][1000 genomes]
rs7298381	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7307156	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7312128	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312698	0.82[EUR][1000 genomes]
rs7314141	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7484762	0.81[CEU][hapmap]
rs7964583	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7976195	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs901599	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[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	nsv438201	chr12:32523455-32531212	Weak transcription Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7298319	BICD1	cis	parietal	SCAN

Chromatin state (count:26 , 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	chr12:32492200-32530400	Weak transcription	Thymus	Thymus
3	chr12:32492400-32532000	Weak transcription	Brain Angular Gyrus	brain
4	chr12:32494200-32533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:32518800-32531800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:32519000-32530400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:32519200-32532000	Weak transcription	NHDF-Ad	bronchial
8	chr12:32520800-32530600	Weak transcription	HSMMtube	muscle
9	chr12:32520800-32532400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:32522400-32532200	Weak transcription	Osteobl	bone
11	chr12:32522600-32530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:32522600-32530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:32522600-32535800	Weak transcription	Fetal Brain Female	brain
14	chr12:32522800-32532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:32529400-32530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:32529800-32530800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:32529800-32532000	Weak transcription	Ovary	ovary
18	chr12:32530000-32530600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:32530000-32530800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:32530000-32530800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:32530000-32530800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:32530000-32530800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr12:32530000-32530800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:32530000-32530800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:32530200-32530600	Enhancers	HSMM	muscle
26	chr12:32530200-32530800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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