Variant report

Variant	rs842
Chromosome Location	chr11:33731406-33731407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:33722591..33725977-chr11:33729219..33731745,3	MCF-7	breast:
2	chr11:33730057..33732913-chr11:33741218..33744001,2	MCF-7	breast:
3	chr11:33713906..33715824-chr11:33729975..33731538,2	MCF-7	breast:
4	chr11:33730241..33733771-chr11:33754827..33758431,3	K562	blood:
5	chr11:33722219..33726232-chr11:33726761..33732163,6	K562	blood:
6	chr11:33728871..33731814-chr11:33757804..33759607,3	MCF-7	breast:
7	chr11:33729551..33732086-chr11:33743744..33746634,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C11orf41-1	chr11:33731100-33731568	ENSG00000254549.1

No data

Variant related genes	Relation type
ENSG00000205177	Chromatin interaction
ENSG00000085063	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1047581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11032363	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs11032374	0.82[ASN][1000 genomes]
rs1112840	0.82[ASN][1000 genomes]
rs12360810	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1402953	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs1546727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2901375	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3181274	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs34944910	0.82[ASN][1000 genomes]
rs35162575	0.82[ASN][1000 genomes]
rs36093484	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4755893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4755894	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56113937	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56399849	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7117382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131663	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832113	chr11:33609202-33767781	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs842	CAPRIN1	cis	cerebellum	SCAN
rs842	HIPK3	cis	cerebellum	SCAN
rs842	FSHB	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33723000-33746000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:33723200-33737400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:33723200-33744400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:33723200-33744400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:33723400-33735000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:33723400-33741400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:33723400-33745000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:33723400-33745800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:33723400-33746000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:33723400-33753400	Weak transcription	Primary B cells from cord blood	blood
11	chr11:33725600-33731800	Genic enhancers	Left Ventricle	heart
12	chr11:33725800-33732000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:33725800-33732200	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr11:33726000-33731600	Genic enhancers	HMEC	breast
15	chr11:33726000-33732000	Genic enhancers	A549	lung
16	chr11:33726000-33732400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:33726000-33733200	Strong transcription	Fetal Stomach	stomach
18	chr11:33726200-33732400	Genic enhancers	HUVEC	blood vessel
19	chr11:33726400-33731600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:33726400-33732000	Genic enhancers	Hela-S3	cervix
21	chr11:33726400-33739800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:33726600-33731600	Genic enhancers	Adipose Nuclei	Adipose
23	chr11:33726600-33732000	Strong transcription	Aorta	Aorta
24	chr11:33726600-33732000	Strong transcription	Thymus	Thymus
25	chr11:33726600-33734200	Strong transcription	K562	blood
26	chr11:33726800-33731800	Strong transcription	Ovary	ovary
27	chr11:33726800-33736000	Strong transcription	HSMMtube	muscle
28	chr11:33726800-33741400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:33727000-33732200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr11:33727000-33735000	Strong transcription	NH-A	brain
31	chr11:33727000-33738200	Strong transcription	HSMM	muscle
32	chr11:33727200-33731600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:33727200-33732400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:33728000-33731800	Genic enhancers	NHLF	lung
35	chr11:33728200-33732200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr11:33728200-33736000	Strong transcription	Fetal Thymus	thymus
37	chr11:33728200-33744000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:33728400-33732000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:33728400-33732200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr11:33728400-33744600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:33728600-33732000	Strong transcription	Fetal Lung	lung
42	chr11:33728600-33732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:33728600-33736000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:33728600-33738200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:33728600-33745000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:33728800-33732000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
47	chr11:33729200-33731800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:33729200-33731800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:33729200-33732200	Strong transcription	Brain Anterior Caudate	brain
50	chr11:33729200-33732400	Strong transcription	Liver	Liver

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