Variant report

Variant	rs11871031
Chromosome Location	chr17:45416538-45416539
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45414278..45416918-chr17:45428922..45430523,2	K562	blood:
2	chr17:45406105..45410563-chr17:45415777..45418447,5	K562	blood:
3	chr17:45402601..45404438-chr17:45415492..45418430,2	K562	blood:

Variant related genes	Relation type
ENSG00000178852	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11079771	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11867192	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11867253	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11867373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11867513	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11867589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869439	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869487	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11869768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11869835	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11870176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11870781	0.84[JPT][hapmap]
rs11870948	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11871477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12051709	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12051795	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12051799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16941751	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16941771	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16941855	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs16941861	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2292344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317676	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs28376443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3744453	1.00[YRI][hapmap]
rs3785870	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3785873	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs73322309	0.80[ASN][1000 genomes]
rs9897801	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv962445	chr17:45397004-45428018	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1062096	chr17:45416538-45518683	Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11871031	PIP4K2B	trans	brain	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45402000-45428600	Weak transcription	Spleen	Spleen
2	chr17:45402000-45442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:45402200-45416800	Weak transcription	Lung	lung
4	chr17:45402200-45420400	Weak transcription	Pancreas	Pancrea
5	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
7	chr17:45402400-45419400	Weak transcription	Liver	Liver
8	chr17:45402400-45419600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:45402400-45421200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr17:45402400-45421400	Weak transcription	Fetal Kidney	kidney
11	chr17:45402400-45421600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr17:45402400-45423400	Weak transcription	NHDF-Ad	bronchial
13	chr17:45402400-45424200	Weak transcription	Fetal Brain Male	brain
14	chr17:45402400-45427200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:45402400-45428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr17:45402400-45433600	Weak transcription	Fetal Heart	heart
17	chr17:45402400-45433600	Weak transcription	Fetal Intestine Small	intestine
18	chr17:45402400-45433600	Weak transcription	Fetal Stomach	stomach
19	chr17:45402400-45435800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr17:45402400-45436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:45402600-45416800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:45402600-45422200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:45402600-45423000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr17:45402600-45423400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:45402600-45424600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr17:45402600-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr17:45402800-45422400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
29	chr17:45403000-45429400	Weak transcription	Placenta	Placenta
30	chr17:45407600-45435800	Weak transcription	Fetal Intestine Large	intestine
31	chr17:45408200-45421000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr17:45409200-45425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:45409400-45419600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:45411200-45419000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr17:45411200-45424000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:45411400-45419800	Weak transcription	Fetal Lung	lung
37	chr17:45411600-45468200	Weak transcription	Left Ventricle	heart
38	chr17:45412400-45463400	Weak transcription	Gastric	stomach
39	chr17:45413400-45419200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:45413400-45419400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:45413400-45421600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr17:45413400-45423800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:45413400-45463800	Weak transcription	Ovary	ovary
44	chr17:45413600-45416600	Weak transcription	HUVEC	blood vessel
45	chr17:45415200-45418600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr17:45415200-45419600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:45415200-45421600	Weak transcription	Adipose Nuclei	Adipose
48	chr17:45415400-45421600	Weak transcription	Primary B cells from cord blood	blood

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