Variant report

Variant	rs7315797
Chromosome Location	chr12:32558994-32558995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32552514..32555337-chr12:32557035..32560074,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045751	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771942	0.81[AMR][1000 genomes]
rs10844197	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844198	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1128591	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs167806	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs186568	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs188978	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs188979	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2062600	0.87[ASN][1000 genomes]
rs2253235	0.85[ASN][1000 genomes]
rs2253237	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253238	0.80[ASN][1000 genomes]
rs2253247	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2450506	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2455004	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2632326	0.80[AMR][1000 genomes]
rs2632330	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2632337	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2632363	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2651365	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2651366	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2651367	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2651368	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2651371	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2651377	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2651380	0.80[AMR][1000 genomes]
rs2728675	0.87[ASN][1000 genomes]
rs2728676	0.86[ASN][1000 genomes]
rs2728678	0.86[ASN][1000 genomes]
rs2728679	0.82[ASN][1000 genomes]
rs2728689	0.86[ASN][1000 genomes]
rs2728690	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733683	0.86[ASN][1000 genomes]
rs2733694	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733696	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733698	0.82[ASN][1000 genomes]
rs2733703	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733704	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733705	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2931554	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs325418	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs325419	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs325420	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs325421	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs325423	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs325424	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931622	0.87[ASN][1000 genomes]
rs4931624	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4931625	0.87[ASN][1000 genomes]
rs56146365	0.81[AMR][1000 genomes]
rs7312698	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315762	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7963401	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	nsv469347	chr12:32555846-32602079	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv558189	chr12:32555846-32602079	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3344698	chr12:32558775-32559374	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7315797	BICD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32553400-32572200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:32553400-32572200	Weak transcription	HSMMtube	muscle
3	chr12:32553400-32572400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:32553600-32572600	Weak transcription	Esophagus	oesophagus
5	chr12:32553800-32571600	Weak transcription	Left Ventricle	heart
6	chr12:32554000-32572200	Weak transcription	Right Ventricle	heart
7	chr12:32554200-32559600	Weak transcription	A549	lung
8	chr12:32554200-32561200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:32554200-32566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:32554200-32571800	Weak transcription	Ovary	ovary
11	chr12:32554200-32573800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:32554400-32559800	Weak transcription	Psoas Muscle	Psoas
13	chr12:32554600-32572400	Weak transcription	Fetal Intestine Large	intestine
14	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:32555400-32571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:32555400-32572000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:32555600-32571400	Weak transcription	Lung	lung
18	chr12:32556000-32571800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:32556200-32561600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:32556400-32561600	Weak transcription	Fetal Intestine Small	intestine
21	chr12:32556400-32562600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:32556400-32571600	Weak transcription	HMEC	breast
23	chr12:32556600-32561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:32557000-32561400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:32557000-32563400	Weak transcription	Pancreas	Pancrea
26	chr12:32557200-32561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:32557400-32561600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:32557400-32571200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:32557600-32560200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:32557600-32560400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:32557600-32561200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:32557600-32561600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:32557600-32563200	Weak transcription	NHEK	skin
34	chr12:32558200-32559200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr12:32558200-32559800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr12:32558400-32559000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr12:32558400-32559200	Enhancers	Gastric	stomach
38	chr12:32558600-32561400	Weak transcription	Stomach Mucosa	stomach
39	chr12:32558800-32560200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:32558800-32562800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:32558800-32566400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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