Variant report

Variant	rs7941341
Chromosome Location	chr11:9038925-9038926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9027002..9028615-chr11:9038847..9041783,2	K562	blood:
2	chr11:9038205..9041771-chr11:9047082..9049951,3	MCF-7	breast:
3	chr11:9033737..9035999-chr11:9038793..9040438,2	MCF-7	breast:
4	chr11:9037545..9039567-chr11:9040874..9042397,2	K562	blood:

Variant related genes	Relation type
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10840170	1.00[CHB][hapmap]
rs10840186	1.00[CHB][hapmap]
rs11042196	1.00[CHB][hapmap]
rs11042197	1.00[CHB][hapmap]
rs11042215	1.00[CHB][hapmap]
rs11042217	1.00[CHB][hapmap]
rs1136966	1.00[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607384	1.00[CHB][hapmap]
rs12794962	0.82[MEX][hapmap]
rs12796375	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960181	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969627	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984775	1.00[CHB][hapmap];0.96[GIH][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984790	0.90[EUR][1000 genomes]
rs2060157	1.00[ASN][1000 genomes]
rs2133215	1.00[CHB][hapmap]
rs2173406	1.00[CHB][hapmap]
rs2568047	0.82[MEX][hapmap]
rs2653558	1.00[CHB][hapmap]
rs2653574	1.00[CHB][hapmap]
rs2653609	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2742483	1.00[ASN][1000 genomes]
rs34004082	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34191466	1.00[ASN][1000 genomes]
rs35578021	1.00[ASN][1000 genomes]
rs4061640	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910443	1.00[CHB][hapmap]
rs56277831	1.00[ASN][1000 genomes]
rs6486138	1.00[CHB][hapmap]
rs7108116	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7110170	0.82[AMR][1000 genomes]
rs7113467	1.00[CHB][hapmap]
rs7114013	1.00[CHB][hapmap]
rs7125458	0.82[MEX][hapmap]
rs7129049	1.00[CHB][hapmap]
rs7130454	1.00[ASN][1000 genomes]
rs71476814	1.00[ASN][1000 genomes]
rs72856032	1.00[ASN][1000 genomes]
rs7396115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7396130	1.00[CHB][hapmap]
rs7396541	1.00[CHB][hapmap]
rs7396840	1.00[CHB][hapmap]
rs7936201	1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945759	1.00[CHB][hapmap]
rs7949022	1.00[CHB][hapmap]
rs7949349	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7941341	CSNK2A1P	cis	cerebellum	SCAN
rs7941341	STK33	cis	cerebellum	SCAN
rs7941341	RPL27A	cis	cerebellum	SCAN
rs7941341	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs7941341	RPL27A	cis	parietal	SCAN
rs7941341	PRKCDBP	cis	parietal	SCAN
rs7941341	HBD	cis	cerebellum	SCAN
rs7941341	ADM	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9034600-9041600	Weak transcription	Gastric	stomach
2	chr11:9035200-9051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:9036400-9039800	Enhancers	Fetal Muscle Leg	muscle
4	chr11:9036600-9048400	Weak transcription	Pancreas	Pancrea
5	chr11:9037000-9040000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:9037200-9039600	Enhancers	Fetal Stomach	stomach
7	chr11:9037200-9040000	Enhancers	Adipose Nuclei	Adipose
8	chr11:9037400-9039000	Enhancers	Spleen	Spleen
9	chr11:9037400-9039200	Enhancers	Stomach Smooth Muscle	stomach
10	chr11:9037400-9039800	Enhancers	Left Ventricle	heart
11	chr11:9037400-9039800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr11:9037400-9040000	Enhancers	Psoas Muscle	Psoas
13	chr11:9037400-9040000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:9037600-9039000	Enhancers	Brain Anterior Caudate	brain
15	chr11:9037600-9039200	Weak transcription	Osteobl	bone
16	chr11:9037600-9039400	Weak transcription	HSMM	muscle
17	chr11:9037600-9039600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:9037600-9039600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr11:9037600-9039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:9037600-9041600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:9037600-9042200	Weak transcription	Right Ventricle	heart
22	chr11:9037600-9045000	Weak transcription	Fetal Brain Male	brain
23	chr11:9037800-9039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:9037800-9039000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:9037800-9039200	Enhancers	Primary T cells from cord blood	blood
26	chr11:9037800-9039600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:9038000-9039000	Enhancers	Duodenum Mucosa	Duodenum
28	chr11:9038000-9039600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr11:9038000-9039800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:9038000-9039800	Enhancers	Placenta	Placenta
31	chr11:9038200-9039000	Enhancers	Lung	lung
32	chr11:9038200-9039400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:9038200-9039400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:9038200-9039600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:9038200-9039600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:9038200-9039600	Enhancers	HUVEC	blood vessel
37	chr11:9038200-9039800	Enhancers	GM12878-XiMat	blood
38	chr11:9038200-9041400	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:9038200-9045200	Weak transcription	HSMMtube	muscle
40	chr11:9038200-9064000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:9038400-9039200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:9038400-9039600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr11:9038400-9039800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:9038400-9040000	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:9038400-9040400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr11:9038600-9039000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr11:9038600-9039200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr11:9038600-9039200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:9038600-9039400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr11:9038600-9039600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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