Variant report

Variant	rs7312869
Chromosome Location	chr12:32554995-32554996
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10771944	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10844194	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10844202	0.90[EUR][1000 genomes]
rs11051966	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11051967	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11051980	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11051993	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12815894	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2087166	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61927215	0.86[EUR][1000 genomes]
rs6488053	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299524	0.88[EUR][1000 genomes]
rs7971525	0.86[EUR][1000 genomes]
rs883404	0.88[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	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	nsv469346	chr12:32531220-32587465	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	8 gene(s)	inside rSNPs	diseases
5	nsv558188	chr12:32531220-32587465	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7312869	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32551800-32555200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:32552000-32555200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:32552000-32555400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:32553200-32555600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:32553400-32555200	Active TSS	Duodenum Mucosa	Duodenum
6	chr12:32553400-32555200	Weak transcription	Lung	lung
7	chr12:32553400-32572200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:32553400-32572200	Weak transcription	HSMMtube	muscle
9	chr12:32553400-32572400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:32553600-32555000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:32553600-32555200	Weak transcription	Gastric	stomach
12	chr12:32553600-32555200	Weak transcription	Pancreas	Pancrea
13	chr12:32553600-32556000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:32553600-32572600	Weak transcription	Esophagus	oesophagus
15	chr12:32553800-32556000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:32553800-32571600	Weak transcription	Left Ventricle	heart
17	chr12:32554000-32555200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:32554000-32555200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:32554000-32572200	Weak transcription	Right Ventricle	heart
20	chr12:32554200-32555000	Weak transcription	HUVEC	blood vessel
21	chr12:32554200-32555200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr12:32554200-32555600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:32554200-32556000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:32554200-32556000	Enhancers	NHEK	skin
25	chr12:32554200-32559600	Weak transcription	A549	lung
26	chr12:32554200-32561200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:32554200-32566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:32554200-32571800	Weak transcription	Ovary	ovary
29	chr12:32554200-32573800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:32554400-32555200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:32554400-32555200	Enhancers	Placenta	Placenta
32	chr12:32554400-32555800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:32554400-32556800	Weak transcription	Colonic Mucosa	Colon
34	chr12:32554400-32559800	Weak transcription	Psoas Muscle	Psoas
35	chr12:32554600-32555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:32554600-32555200	Weak transcription	Adipose Nuclei	Adipose
37	chr12:32554600-32555200	Weak transcription	Stomach Mucosa	stomach
38	chr12:32554600-32555200	Weak transcription	HMEC	breast
39	chr12:32554600-32555600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:32554600-32556000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:32554600-32556200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:32554600-32557000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:32554600-32572400	Weak transcription	Fetal Intestine Large	intestine
44	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:32554800-32555000	Weak transcription	Fetal Intestine Small	intestine
46	chr12:32554800-32555200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:32554800-32555200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:32554800-32555200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:32554800-32555200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr12:32554800-32555800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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