Variant report

Variant	rs2955934
Chromosome Location	chr11:34193578-34193579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34192703..34198960-chr11:34377862..34381176,7	MCF-7	breast:
2	chr11:34185430..34188378-chr11:34191219..34194935,5	MCF-7	breast:
3	chr11:34189648..34198426-chr11:34377718..34382191,19	MCF-7	breast:
4	chr11:34186526..34189474-chr11:34192955..34194776,3	MCF-7	breast:
5	chr11:34168126..34171027-chr11:34193245..34194980,2	MCF-7	breast:
6	chr11:34187334..34191068-chr11:34191112..34197188,7	K562	blood:

Variant related genes	Relation type
ENSG00000166016	Chromatin interaction
ENSG00000135372	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10768049	0.94[EUR][1000 genomes]
rs10836157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11032537	0.88[ASN][1000 genomes]
rs1321017	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321018	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1321019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1569774	0.96[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2143868	0.81[CHD][hapmap]
rs2467383	0.87[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2473918	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2955935	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957492	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2982606	0.87[CEU][hapmap];0.83[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2982607	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2982608	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34427038	0.81[ASN][1000 genomes]
rs59698692	0.94[ASN][1000 genomes]
rs7102200	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120934	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7121122	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7121208	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7121259	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7124122	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7937404	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950979	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs910256	0.86[JPT][hapmap]
rs910257	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[MKK][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	nsv523431	chr11:34192092-34199849	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2955934	C11orf41	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34169600-34196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:34173200-34195600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr11:34176800-34195600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:34177000-34196200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:34177400-34195400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:34177600-34194600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:34177600-34196200	Weak transcription	Primary T cells from cord blood	blood
8	chr11:34177800-34195800	Weak transcription	Spleen	Spleen
9	chr11:34177800-34196000	Weak transcription	GM12878-XiMat	blood
10	chr11:34178800-34195200	Weak transcription	Hela-S3	cervix
11	chr11:34179200-34195400	Weak transcription	Adipose Nuclei	Adipose
12	chr11:34179400-34196000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:34179600-34193600	Strong transcription	Liver	Liver
14	chr11:34180000-34195200	Strong transcription	HepG2	liver
15	chr11:34180600-34195400	Weak transcription	Fetal Thymus	thymus
16	chr11:34181400-34195400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:34182200-34195400	Weak transcription	Osteobl	bone
18	chr11:34182800-34196000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:34183000-34195200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:34183600-34198000	Weak transcription	Fetal Lung	lung
21	chr11:34183800-34194400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:34184200-34195400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:34184200-34195400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:34184200-34195800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:34184400-34195400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:34184600-34196000	Weak transcription	Gastric	stomach
27	chr11:34184800-34195400	Weak transcription	Brain Anterior Caudate	brain
28	chr11:34185000-34195400	Weak transcription	Brain Angular Gyrus	brain
29	chr11:34187000-34195400	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:34188400-34195000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:34188400-34196200	Weak transcription	Esophagus	oesophagus
32	chr11:34189200-34195200	Weak transcription	Brain Germinal Matrix	brain
33	chr11:34189600-34195400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:34189600-34195800	Weak transcription	Thymus	Thymus
35	chr11:34190200-34195600	Weak transcription	Fetal Brain Female	brain
36	chr11:34190400-34194600	Weak transcription	Fetal Stomach	stomach
37	chr11:34190400-34195000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:34190400-34195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:34190400-34195600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:34190400-34195800	Weak transcription	Pancreas	Pancrea
41	chr11:34190600-34195800	Weak transcription	NH-A	brain
42	chr11:34190600-34196000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:34191400-34194600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:34191400-34195000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:34191600-34194600	Weak transcription	Lung	lung
46	chr11:34191800-34195000	Strong transcription	Placenta	Placenta
47	chr11:34191800-34195400	Weak transcription	A549	lung
48	chr11:34191800-34195800	Weak transcription	Right Ventricle	heart
49	chr11:34191800-34195800	Weak transcription	HUVEC	blood vessel
50	chr11:34192000-34193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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