Variant report

Variant	rs7966841
Chromosome Location	chr12:39784956-39784957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39771043..39772683-chr12:39784560..39786078,2	MCF-7	breast:
2	chr12:39784633..39788139-chr12:39834968..39838023,4	MCF-7	breast:
3	chr12:39783416..39787534-chr12:39834798..39837698,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11172144	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs11172162	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs11172687	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs12227286	1.00[JPT][hapmap]
rs12228013	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs1512941	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512943	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17126997	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17127029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127094	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127100	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17127138	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2137495	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271478	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2292491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294600	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4620763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56858582	0.84[AFR][1000 genomes]
rs57196300	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59967849	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039034	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133376	0.90[JPT][hapmap]
rs7135918	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086885	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088816	0.83[ASN][1000 genomes]
rs7309234	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7310178	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7312611	0.90[JPT][hapmap]
rs7956823	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7970819	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970944	0.83[ASN][1000 genomes]
rs7976275	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963637	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7966841	ABCD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
3	chr12:39778800-39786000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:39778800-39787200	Weak transcription	Right Ventricle	heart
5	chr12:39779000-39786000	Weak transcription	Left Ventricle	heart
6	chr12:39779200-39786200	Weak transcription	Psoas Muscle	Psoas
7	chr12:39780200-39787400	Weak transcription	Liver	Liver
8	chr12:39780400-39789800	Weak transcription	HepG2	liver
9	chr12:39781200-39791400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:39781400-39800200	Weak transcription	Brain Angular Gyrus	brain
11	chr12:39781600-39785800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:39781600-39785800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:39781600-39786200	Weak transcription	Right Atrium	heart
14	chr12:39781600-39786400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:39781800-39787000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:39782000-39786000	Weak transcription	Brain Anterior Caudate	brain
17	chr12:39782200-39796800	Weak transcription	A549	lung
18	chr12:39782400-39785000	Weak transcription	Fetal Heart	heart
19	chr12:39782400-39785400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:39782400-39785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:39782600-39786000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:39783200-39785000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:39783800-39786200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:39784000-39786000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:39784000-39786200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:39784000-39786200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:39784200-39785800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:39784400-39785000	Enhancers	HMEC	breast
29	chr12:39784600-39785000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:39784600-39785200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:39784600-39785200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:39784600-39785200	Enhancers	NHEK	skin
33	chr12:39784600-39786000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:39784600-39787600	Enhancers	Brain Germinal Matrix	brain
35	chr12:39784800-39785200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:39784800-39785400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:39784800-39786000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:39784800-39786000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:39784800-39786000	Enhancers	Fetal Brain Male	brain
40	chr12:39784800-39786200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:39784800-39789400	Enhancers	Cortex derived primary cultured neurospheres	brain

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