Variant report

Variant	rs11602256
Chromosome Location	chr11:68144283-68144284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:68142620..68145092-chr11:68154931..68156439,2	K562	blood:
2	chr11:68078491..68080694-chr11:68144064..68145682,2	MCF-7	breast:
3	chr11:68139963..68143700-chr11:68143791..68147570,5	K562	blood:
4	chr11:68109553..68111761-chr11:68141743..68145127,3	MCF-7	breast:
5	chr11:68133350..68135740-chr11:68141722..68144465,3	MCF-7	breast:
6	chr11:68099361..68102252-chr11:68142403..68144649,2	MCF-7	breast:
7	chr11:68142032..68143700-chr11:68144005..68145660,2	K562	blood:

Variant related genes	Relation type
ENSG00000162337	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10896321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11228225	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823032	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11826287	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs12222261	0.90[ASN][1000 genomes]
rs160607	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1784237	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2508838	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs312778	0.87[MEX][hapmap]
rs312779	0.86[MEX][hapmap]
rs312783	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs312788	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs312792	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs314773	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs314775	0.86[JPT][hapmap]
rs3781590	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57197891	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs587808	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs628115	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs643892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66787665	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs671191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74744	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv897861	chr11:68129606-68196830	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11602256	DNAJC4	cis	parietal	SCAN
rs11602256	C11orf59	cis	cerebellum	SCAN
rs11602256	RBM4B	cis	cerebellum	SCAN
rs11602256	FKBP2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68121600-68148200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:68121800-68156400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:68124800-68146600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:68128200-68153800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:68129800-68153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:68135200-68147600	Weak transcription	Primary T cells from cord blood	blood
7	chr11:68135200-68153400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:68135200-68153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:68136200-68153400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:68136600-68145600	Enhancers	Left Ventricle	heart
11	chr11:68136800-68152800	Weak transcription	Dnd41	blood
12	chr11:68137000-68156400	Weak transcription	K562	blood
13	chr11:68139200-68144400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr11:68139200-68145800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:68139600-68156400	Weak transcription	Hela-S3	cervix
16	chr11:68140000-68144600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:68140000-68147600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:68140000-68147800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:68140000-68150200	Enhancers	Lung	lung
20	chr11:68140000-68153400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr11:68140200-68153600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:68141200-68148200	Weak transcription	Aorta	Aorta
23	chr11:68141400-68153400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:68141800-68145400	Genic enhancers	Fetal Stomach	stomach
25	chr11:68142000-68145000	Genic enhancers	Right Ventricle	heart
26	chr11:68142000-68147600	Weak transcription	Fetal Thymus	thymus
27	chr11:68142200-68144600	Weak transcription	A549	lung
28	chr11:68142200-68146600	Weak transcription	Fetal Kidney	kidney
29	chr11:68142200-68146800	Weak transcription	GM12878-XiMat	blood
30	chr11:68142400-68144400	Strong transcription	Thymus	Thymus
31	chr11:68142400-68146000	Genic enhancers	Fetal Muscle Leg	muscle
32	chr11:68142400-68146200	Strong transcription	Fetal Intestine Large	intestine
33	chr11:68142400-68146600	Weak transcription	NH-A	brain
34	chr11:68142400-68147600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:68142400-68147800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:68142600-68144800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:68142600-68144800	Strong transcription	Fetal Intestine Small	intestine
38	chr11:68142600-68145800	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr11:68142600-68146600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:68142600-68146600	Weak transcription	NHLF	lung
41	chr11:68142600-68146800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:68142600-68146800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:68142600-68146800	Weak transcription	Osteobl	bone
44	chr11:68142600-68147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:68142600-68148000	Weak transcription	Fetal Brain Female	brain
46	chr11:68142600-68148200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:68142600-68179000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:68142800-68144400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:68142800-68144400	Strong transcription	HepG2	liver
50	chr11:68142800-68145000	Weak transcription	Rectal Mucosa Donor 29	rectum

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