Variant report

Variant	rs11959914
Chromosome Location	chr5:177857479-177857480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177851066..177853109-chr5:177854719..177857640,2	MCF-7	breast:
2	chr5:177855622..177857824-chr5:177858602..177861991,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10039491	1.00[JPT][hapmap]
rs10479493	0.83[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs12652427	0.83[CEU][hapmap]
rs1391654	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs17648414	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546628	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2546629	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2647688	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2647693	1.00[JPT][hapmap]
rs2672820	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2672843	1.00[JPT][hapmap]
rs4383738	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4976776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976777	1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs55662845	0.87[AMR][1000 genomes]
rs56135911	0.87[AMR][1000 genomes]
rs6422348	0.91[YRI][hapmap]
rs7711430	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11959914	TRIM41	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177848800-177859800	Strong transcription	Thymus	Thymus
2	chr5:177853200-177858400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:177854200-177857600	Enhancers	Fetal Lung	lung
4	chr5:177855600-177858200	Enhancers	Pancreas	Pancrea
5	chr5:177855800-177857600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:177856000-177861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:177856400-177857600	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr5:177856400-177857600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr5:177856400-177861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:177856600-177857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:177856600-177861000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:177856800-177861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:177856800-177861600	Weak transcription	Brain Angular Gyrus	brain
14	chr5:177856800-177861600	Weak transcription	Fetal Heart	heart
15	chr5:177856800-177861800	Weak transcription	Left Ventricle	heart
16	chr5:177856800-177887200	Weak transcription	Right Atrium	heart
17	chr5:177857000-177859400	Weak transcription	Right Ventricle	heart
18	chr5:177857000-177859600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:177857000-177861600	Weak transcription	Psoas Muscle	Psoas
20	chr5:177857000-177862600	Weak transcription	Gastric	stomach
21	chr5:177857000-177863800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:177857200-177858000	Weak transcription	Lung	lung
23	chr5:177857200-177858400	Weak transcription	Fetal Stomach	stomach
24	chr5:177857200-177859200	Strong transcription	Fetal Thymus	thymus
25	chr5:177857200-177859400	Weak transcription	Liver	Liver
26	chr5:177857200-177859600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:177857200-177862000	Weak transcription	Fetal Kidney	kidney
28	chr5:177857400-177857600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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