Variant report

Variant	rs12442096
Chromosome Location	chr15:74038773-74038774
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	chr15:74037382..74039248-chr15:74049351..74051185,2	MCF-7	breast:
2	chr15:74038183..74040978-chr15:74046386..74048785,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1038093	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072438	0.88[ASN][1000 genomes]
rs12440563	0.85[LWK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12913243	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17187183	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2123208	0.88[AFR][1000 genomes]
rs2127018	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28485305	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28505607	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28581503	0.86[ASN][1000 genomes]
rs28594180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655328	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28709470	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4243087	0.84[AFR][1000 genomes]
rs4886520	0.87[ASN][1000 genomes]
rs4887111	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4887161	0.91[AFR][1000 genomes]
rs60833441	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7162423	0.86[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7171779	0.86[ASW][hapmap];0.85[LWK][hapmap]
rs7172656	0.86[ASW][hapmap];0.85[LWK][hapmap]

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	nsv471252	chr15:74006691-74089793	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv569970	chr15:74016622-74059081	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12442096	FEM1B	cis	parietal	SCAN
rs12442096	COMMD4	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74030000-74039200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:74033400-74038800	Weak transcription	Fetal Brain Male	brain
3	chr15:74034000-74038800	Weak transcription	Ovary	ovary
4	chr15:74034400-74038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:74034600-74038800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:74035000-74043000	Strong transcription	Fetal Stomach	stomach
7	chr15:74035400-74038800	Weak transcription	Right Atrium	heart
8	chr15:74035400-74039000	Weak transcription	Left Ventricle	heart
9	chr15:74035600-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:74035600-74039000	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:74035600-74039600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:74035600-74043800	Weak transcription	Esophagus	oesophagus
13	chr15:74035800-74038800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:74035800-74038800	Weak transcription	Right Ventricle	heart
15	chr15:74035800-74039200	Weak transcription	Hela-S3	cervix
16	chr15:74035800-74039400	Weak transcription	A549	lung
17	chr15:74035800-74042400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:74035800-74043200	Weak transcription	Brain Substantia Nigra	brain
19	chr15:74036400-74041200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:74037000-74038800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:74037000-74039000	Enhancers	Brain Germinal Matrix	brain
22	chr15:74037000-74039200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:74037000-74041400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:74037400-74039200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:74037600-74038800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:74037600-74039000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:74037800-74038800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:74037800-74038800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:74037800-74039000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:74037800-74039200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:74038000-74038800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:74038000-74039000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:74038000-74040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:74038000-74040800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:74038200-74040800	Enhancers	Fetal Brain Female	brain
36	chr15:74038400-74039600	Enhancers	Spleen	Spleen
37	chr15:74038600-74039000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:74038600-74039200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:74038600-74039400	Enhancers	Fetal Lung	lung
40	chr15:74038600-74039800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:74038600-74039800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr15:74038600-74039800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr15:74038600-74039800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr15:74038600-74040000	Enhancers	HSMMtube	muscle
45	chr15:74038600-74040200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr15:74038600-74041200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:74038600-74041400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:74038600-74041600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:74038600-74042400	Enhancers	Brain Anterior Caudate	brain

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