Variant report

Variant	rs7972023
Chromosome Location	chr12:32465108-32465109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31835084..31835691-chr12:32464822..32465710,2	MCF-7	breast:
2	chr12:32461768..32463542-chr12:32464006..32465889,2	MCF-7	breast:
3	chr12:32414725..32415274-chr12:32464881..32465588,2	MCF-7	breast:
4	chr12:32213222..32214189-chr12:32464699..32465690,4	MCF-7	breast:
5	chr12:32259422..32259994-chr12:32464784..32465376,2	MCF-7	breast:
6	chr12:32455258..32455874-chr12:32465064..32465668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151746	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10431225	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10431283	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10844179	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10844183	0.86[EUR][1000 genomes]
rs10844184	0.84[EUR][1000 genomes]
rs10844188	0.86[EUR][1000 genomes]
rs11051925	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051928	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051929	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051932	0.86[EUR][1000 genomes]
rs11051934	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051935	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11051936	0.86[EUR][1000 genomes]
rs11051937	0.86[EUR][1000 genomes]
rs11051938	0.86[EUR][1000 genomes]
rs11051939	0.86[EUR][1000 genomes]
rs11051940	0.85[EUR][1000 genomes]
rs11051941	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11051942	0.86[EUR][1000 genomes]
rs11051943	0.87[EUR][1000 genomes]
rs11051944	0.86[EUR][1000 genomes]
rs11051945	0.82[EUR][1000 genomes]
rs11051946	0.82[EUR][1000 genomes]
rs11536026	0.87[EUR][1000 genomes]
rs11833592	0.86[EUR][1000 genomes]
rs12578899	0.86[EUR][1000 genomes]
rs12825052	1.00[YRI][hapmap]
rs16919727	0.86[EUR][1000 genomes]
rs1972033	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1972438	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2036304	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291420	0.86[EUR][1000 genomes]
rs2291421	0.86[EUR][1000 genomes]
rs2388988	0.82[EUR][1000 genomes]
rs2388989	0.82[EUR][1000 genomes]
rs2892655	0.82[EUR][1000 genomes]
rs3748275	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3748276	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3789975	0.86[EUR][1000 genomes]
rs3816819	0.86[EUR][1000 genomes]
rs4316592	0.86[EUR][1000 genomes]
rs4474533	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4604975	0.82[EUR][1000 genomes]
rs4931012	0.88[EUR][1000 genomes]
rs4931621	0.86[EUR][1000 genomes]
rs58236386	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58926489	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58959894	0.81[EUR][1000 genomes]
rs60221824	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6488044	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7300646	0.84[EUR][1000 genomes]
rs7956708	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7962680	0.84[EUR][1000 genomes]
rs7963887	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974653	0.84[EUR][1000 genomes]
rs7977938	0.88[EUR][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	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7972023	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32443800-32480400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:32449200-32480400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:32449600-32490200	Weak transcription	HSMMtube	muscle
4	chr12:32450400-32480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:32455200-32480400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:32456400-32480400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:32457200-32494400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:32459200-32480200	Weak transcription	Primary B cells from cord blood	blood
9	chr12:32459200-32480800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:32459400-32480600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:32460400-32480600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:32460400-32514600	Weak transcription	HMEC	breast
13	chr12:32460600-32480600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:32460800-32480400	Weak transcription	Osteobl	bone
15	chr12:32461000-32480800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:32461200-32480200	Weak transcription	HSMM	muscle
17	chr12:32461400-32480000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:32461400-32480200	Weak transcription	NH-A	brain
19	chr12:32461600-32472000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:32461800-32480400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:32462400-32465200	Enhancers	Fetal Intestine Large	intestine
22	chr12:32463000-32480200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:32463200-32480200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:32463600-32466600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:32463600-32466600	Weak transcription	Ovary	ovary
26	chr12:32463800-32469400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:32463800-32478400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:32464000-32465200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:32464600-32465200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:32464600-32465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:32464600-32465200	Flanking Active TSS	HUVEC	blood vessel
32	chr12:32464600-32465400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:32464800-32465200	Enhancers	Brain Hippocampus Middle	brain
34	chr12:32464800-32465200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:32464800-32465200	Enhancers	Fetal Kidney	kidney
36	chr12:32464800-32465200	Enhancers	Dnd41	blood
37	chr12:32464800-32465400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr12:32464800-32465400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:32464800-32465400	Enhancers	Adipose Nuclei	Adipose
40	chr12:32464800-32465600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:32464800-32465600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:32464800-32465600	Enhancers	A549	lung
43	chr12:32465000-32465200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:32465000-32465200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:32465000-32465200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:32465000-32465200	Enhancers	Primary hematopoietic stem cells	blood
47	chr12:32465000-32465200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:32465000-32465200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr12:32465000-32465200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:32465000-32465200	Weak transcription	Brain Substantia Nigra	brain

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