Variant report

Variant	rs11602501
Chromosome Location	chr11:57073233-57073234
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57072498-57073353	U87	brain:	n/a	n/a
2	POLR2A	chr11:57072659-57073379	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57070443..57073281-chr11:57104289..57106679,2	MCF-7	breast:
2	chr11:57072221..57074668-chr11:57092202..57093754,2	K562	blood:
3	chr11:57065084..57068349-chr11:57071009..57074536,5	K562	blood:
4	chr11:57072533..57077787-chr11:57091126..57096114,6	MCF-7	breast:

Variant related genes	Relation type
TNKS1BP1	TF binding region
ENSG00000149115	Chromatin interaction
ENSG00000109991	Chromatin interaction
ENSG00000254662	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10732882	0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[MKK][hapmap];0.83[ASN][1000 genomes]
rs10792083	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10792085	0.80[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10896596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896599	0.87[EUR][1000 genomes]
rs10896601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896602	0.80[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10896609	0.82[ASN][1000 genomes]
rs11228971	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11228988	0.90[ASN][1000 genomes]
rs11604373	0.89[ASN][1000 genomes]
rs17573746	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1939496	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2511029	0.82[EUR][1000 genomes]
rs2846051	0.83[EUR][1000 genomes]
rs3935069	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939129	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939131	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939134	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5012051	0.96[CEU][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs522656	0.80[EUR][1000 genomes]
rs55637147	0.83[ASN][1000 genomes]
rs590240	0.81[EUR][1000 genomes]
rs7130020	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928905	0.89[ASN][1000 genomes]
rs7931298	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7936545	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7943761	0.90[ASN][1000 genomes]
rs7943915	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948723	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11602501	MS4A3	cis	cerebellum	SCAN
rs11602501	GLYATL2	cis	parietal	SCAN
rs11602501	OR9I1	cis	cerebellum	SCAN
rs11602501	OR4C6	cis	parietal	SCAN
rs11602501	OR5M9	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57052400-57078200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57067200-57078400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:57067400-57078400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:57067400-57079000	Weak transcription	Primary B cells from cord blood	blood
5	chr11:57067600-57078400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:57067800-57078000	Weak transcription	Fetal Heart	heart
7	chr11:57067800-57078400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:57068400-57073600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:57068400-57078400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:57068400-57081600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:57068600-57073600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:57068800-57078200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr11:57068800-57078200	Weak transcription	Fetal Brain Male	brain
14	chr11:57069200-57076400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:57069600-57073800	Weak transcription	Fetal Kidney	kidney
16	chr11:57069600-57076800	Weak transcription	Brain Substantia Nigra	brain
17	chr11:57069600-57078400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:57069800-57074000	Weak transcription	Small Intestine	intestine
19	chr11:57069800-57076400	Weak transcription	Fetal Thymus	thymus
20	chr11:57069800-57078200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:57069800-57078600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:57069800-57078600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:57070000-57074600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:57070000-57078200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:57070000-57078400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:57070000-57078600	Weak transcription	Primary T cells from cord blood	blood
27	chr11:57070200-57074800	Weak transcription	Brain Angular Gyrus	brain
28	chr11:57070200-57078200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:57070200-57078400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:57070200-57078600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:57070400-57073800	Strong transcription	Fetal Intestine Large	intestine
32	chr11:57070400-57076200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:57070600-57078000	Genic enhancers	HMEC	breast
34	chr11:57070800-57073800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:57070800-57073800	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr11:57070800-57075000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:57070800-57075000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:57070800-57075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:57070800-57075400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:57070800-57076000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:57070800-57077600	Weak transcription	Thymus	Thymus
42	chr11:57071000-57073800	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr11:57071000-57073800	Enhancers	Liver	Liver
44	chr11:57071000-57074600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:57071000-57075400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:57071000-57076200	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:57071000-57077400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:57071000-57078000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:57071200-57073400	Enhancers	Spleen	Spleen
50	chr11:57071200-57074600	Genic enhancers	Adipose Nuclei	Adipose

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