Variant report

Variant	rs6488049
Chromosome Location	chr12:32527126-32527127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10771941	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771942	0.85[EUR][1000 genomes]
rs10771943	0.83[AFR][1000 genomes]
rs1809601	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56146365	0.84[EUR][1000 genomes]
rs6488048	0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7135763	0.86[ASN][1000 genomes]
rs7298319	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298381	0.83[EUR][1000 genomes]
rs7307156	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307458	0.81[ASN][1000 genomes]
rs7312128	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7314141	0.92[ASN][1000 genomes]
rs7964583	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7976195	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs901599	0.94[AFR][1000 genomes];0.88[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
rs6488049	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 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	chr12:32492200-32527400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:32492200-32530400	Weak transcription	Thymus	Thymus
4	chr12:32492400-32527200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:32492400-32532000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:32494200-32533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:32518800-32531800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:32519000-32530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:32519000-32530000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:32519000-32530000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:32519000-32530000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:32519000-32530200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:32519000-32530400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:32519200-32530200	Weak transcription	HSMM	muscle
15	chr12:32519200-32532000	Weak transcription	NHDF-Ad	bronchial
16	chr12:32520600-32529800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:32520800-32530600	Weak transcription	HSMMtube	muscle
18	chr12:32520800-32532400	Weak transcription	Fetal Intestine Small	intestine
19	chr12:32522400-32530000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:32522400-32532200	Weak transcription	Osteobl	bone
21	chr12:32522600-32527200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:32522600-32529000	Weak transcription	Ovary	ovary
23	chr12:32522600-32530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:32522600-32530400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:32522600-32535800	Weak transcription	Fetal Brain Female	brain
26	chr12:32522800-32532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:32525800-32529400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:32526400-32527800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:32526800-32527200	Enhancers	Placenta	Placenta
30	chr12:32526800-32527400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:32526800-32527600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:32526800-32527600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:32527000-32527200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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