Variant report

Variant	rs949349
Chromosome Location	chr11:86297189-86297190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86288370..86290389-chr11:86296721..86299519,2	MCF-7	breast:
2	chr11:86287937..86289819-chr11:86294344..86297343,2	MCF-7	breast:
3	chr11:86292598..86295203-chr11:86295582..86300821,4	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11234704	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1945034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1945035	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1808984	chr11:86282680-86301717	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv555678	chr11:86285994-86305977	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs949349	CTSC	cis	cerebellum	SCAN
rs949349	PICALM	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86275400-86299400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:86276400-86299800	Weak transcription	Fetal Brain Male	brain
3	chr11:86286000-86299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:86286400-86298200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:86289800-86303200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:86289800-86303400	Weak transcription	Stomach Mucosa	stomach
7	chr11:86290600-86298200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:86290600-86299400	Weak transcription	Psoas Muscle	Psoas
9	chr11:86290800-86298200	Weak transcription	HMEC	breast
10	chr11:86290800-86299200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:86291400-86298200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:86292000-86303800	Weak transcription	Ovary	ovary
13	chr11:86292200-86297200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:86292200-86298200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr11:86292200-86303200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:86292400-86298600	Weak transcription	Adipose Nuclei	Adipose
17	chr11:86292800-86297400	Weak transcription	Right Atrium	heart
18	chr11:86292800-86298200	Weak transcription	Right Ventricle	heart
19	chr11:86292800-86303800	Weak transcription	Gastric	stomach
20	chr11:86293400-86303800	Weak transcription	Aorta	Aorta
21	chr11:86293800-86299200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:86293800-86299400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:86294000-86299400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:86294000-86299400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:86294200-86299400	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:86294200-86303800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:86294400-86297200	Weak transcription	Fetal Intestine Large	intestine
28	chr11:86294400-86298200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:86294400-86298200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:86294400-86298400	Weak transcription	A549	lung
31	chr11:86294400-86299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:86294400-86299600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:86294400-86303400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:86294600-86299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:86294600-86299200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr11:86295600-86303400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:86295800-86297200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:86296800-86298600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr11:86297000-86299800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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