Variant report

Variant	rs2062600
Chromosome Location	chr12:32556989-32556990
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	chr12:32551819..32553534-chr12:32555515..32557617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1045751	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1058640	0.83[CEU][hapmap]
rs10771940	0.83[CEU][hapmap]
rs10771942	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10771943	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10844193	0.82[CEU][hapmap]
rs10844197	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10844198	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1128591	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs167806	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs186568	0.88[ASN][1000 genomes]
rs188978	0.95[ASN][1000 genomes]
rs188979	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2253235	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253237	0.89[ASN][1000 genomes]
rs2253238	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2253247	0.90[ASN][1000 genomes]
rs2450506	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2455004	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2632330	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2632337	0.90[ASN][1000 genomes]
rs2632363	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2651365	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2651366	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2651367	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2651368	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2651371	0.82[ASN][1000 genomes]
rs2651377	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2728675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728676	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2728678	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2728679	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2728689	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2728690	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2733683	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733694	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733696	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2733698	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2733703	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2733704	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2733705	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2931554	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs325418	0.94[ASN][1000 genomes]
rs325419	0.96[ASN][1000 genomes]
rs325420	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs325421	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs325423	0.86[ASN][1000 genomes]
rs325424	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs325425	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs325426	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs325429	0.83[CEU][hapmap]
rs4931622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931624	0.90[ASN][1000 genomes]
rs4931625	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61927173	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6488048	0.91[CEU][hapmap]
rs7298381	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7312698	0.99[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7314141	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs7315762	0.88[ASN][1000 genomes]
rs7315797	0.87[ASN][1000 genomes]
rs7958506	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7963401	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964583	0.91[CEU][hapmap]
rs7976195	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2062600	BICD1	Cis_1M	lymphoblastoid	RTeQTL
rs2062600	BICD1	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr12:32554600-32557000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:32554600-32572400	Weak transcription	Fetal Intestine Large	intestine
15	chr12:32554600-32593200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:32555200-32557200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr12:32555200-32557600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:32555200-32557600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:32555400-32558400	Weak transcription	Gastric	stomach
20	chr12:32555400-32571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:32555400-32572000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:32555600-32557600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:32555600-32558600	Weak transcription	Adipose Nuclei	Adipose
24	chr12:32555600-32571400	Weak transcription	Lung	lung
25	chr12:32555800-32557000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:32556000-32571800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:32556200-32557600	Enhancers	H9 Cell Line	embryonic stem cell
28	chr12:32556200-32561600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:32556400-32557000	Genic enhancers	H1 Cell Line	embryonic stem cell
30	chr12:32556400-32557000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:32556400-32557200	Weak transcription	NHEK	skin
32	chr12:32556400-32557400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:32556400-32557600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:32556400-32558400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:32556400-32561600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:32556400-32562600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:32556400-32571600	Weak transcription	HMEC	breast
38	chr12:32556600-32557400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:32556600-32558200	Weak transcription	Stomach Mucosa	stomach
40	chr12:32556600-32558400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:32556600-32561400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:32556800-32557000	Enhancers	Pancreas	Pancrea
43	chr12:32556800-32557000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:32556800-32557400	Enhancers	Liver	Liver

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