Variant report

Variant	rs4135066
Chromosome Location	chr12:104366340-104366341
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	chr12:104364267..104367088-chr12:104376743..104378838,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11111861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125322	1.00[ASN][1000 genomes]
rs11611650	1.00[ASN][1000 genomes]
rs1165672	1.00[ASN][1000 genomes]
rs12825687	1.00[ASN][1000 genomes]
rs1385663	1.00[ASN][1000 genomes]
rs167715	1.00[ASN][1000 genomes]
rs167716	1.00[ASN][1000 genomes]
rs1882018	1.00[CEU][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]
rs2243680	1.00[ASN][1000 genomes]
rs2248995	1.00[ASN][1000 genomes]
rs2251215	1.00[ASN][1000 genomes]
rs2252213	1.00[ASN][1000 genomes]
rs2374327	1.00[CEU][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]
rs2439621	1.00[ASN][1000 genomes]
rs2576943	1.00[ASN][1000 genomes]
rs2583224	1.00[ASN][1000 genomes]
rs2583225	1.00[ASN][1000 genomes]
rs2583233	1.00[ASN][1000 genomes]
rs2583234	1.00[ASN][1000 genomes]
rs2583237	1.00[ASN][1000 genomes]
rs2583244	1.00[ASN][1000 genomes]
rs2583258	1.00[ASN][1000 genomes]
rs2583274	1.00[ASN][1000 genomes]
rs2583278	1.00[ASN][1000 genomes]
rs2629750	1.00[ASN][1000 genomes]
rs2700494	1.00[ASN][1000 genomes]
rs2700507	1.00[ASN][1000 genomes]
rs2700517	1.00[ASN][1000 genomes]
rs2722177	1.00[ASN][1000 genomes]
rs2722180	1.00[ASN][1000 genomes]
rs2722194	1.00[ASN][1000 genomes]
rs2723849	1.00[ASN][1000 genomes]
rs2723850	1.00[ASN][1000 genomes]
rs2723853	1.00[ASN][1000 genomes]
rs322104	1.00[ASN][1000 genomes]
rs322109	1.00[ASN][1000 genomes]
rs35140616	1.00[ASN][1000 genomes]
rs4135039	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135040	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135047	1.00[CEU][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]
rs4135048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][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]
rs4135050	1.00[CEU][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]
rs4135059	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4135061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784084	1.00[ASN][1000 genomes]
rs931306	1.00[CEU][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]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv3359723	chr12:104359646-104370785	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4135066	PAH	cis	parietal	SCAN
rs4135066	MYBPC1	cis	cerebellum	SCAN
rs4135066	MAPK11	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104360400-104368000	Weak transcription	Pancreas	Pancrea
2	chr12:104360800-104366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:104360800-104368000	Weak transcription	Lung	lung
4	chr12:104360800-104371200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:104360800-104371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:104360800-104371200	Weak transcription	Colonic Mucosa	Colon
7	chr12:104360800-104371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:104360800-104378600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:104360800-104381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:104361000-104367000	Weak transcription	Fetal Intestine Large	intestine
11	chr12:104361000-104368800	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:104361000-104370800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:104361000-104371000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:104361000-104371000	Weak transcription	Fetal Kidney	kidney
15	chr12:104361000-104372000	Weak transcription	Stomach Mucosa	stomach
16	chr12:104361200-104366800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:104361200-104367000	Weak transcription	Fetal Stomach	stomach
18	chr12:104361200-104367400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:104361200-104369400	Weak transcription	Right Atrium	heart
20	chr12:104361200-104370400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:104361200-104370800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:104361200-104370800	Weak transcription	Fetal Lung	lung
23	chr12:104361200-104371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:104361200-104371000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:104361200-104379400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:104361600-104385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:104361800-104371200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:104362000-104367800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:104362000-104369400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:104362000-104373800	Weak transcription	Psoas Muscle	Psoas
31	chr12:104362000-104382600	Weak transcription	Esophagus	oesophagus
32	chr12:104362000-104384400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
34	chr12:104362200-104366600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:104362200-104370800	Weak transcription	Adipose Nuclei	Adipose
36	chr12:104362200-104371200	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:104362200-104384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:104362400-104367000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:104362400-104367000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:104362400-104369200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:104362400-104371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:104362400-104371000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:104362400-104371200	Weak transcription	Brain Germinal Matrix	brain
44	chr12:104362400-104371400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:104362400-104378000	Weak transcription	Small Intestine	intestine
46	chr12:104362600-104367000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:104362600-104371000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:104362600-104371000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:104363200-104366600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr12:104363200-104367200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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