Variant report

Variant	rs10898950
Chromosome Location	chr11:73600888-73600889
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	chr11:73600327..73602691-chr11:73608708..73610968,2	MCF-7	breast:
2	chr11:73585766..73589510-chr11:73599101..73602813,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181924	Chromatin interaction
ENSG00000175575	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10898948	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11220	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235932	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs11235937	0.83[TSI][hapmap]
rs12284235	0.89[ASW][hapmap];0.82[MEX][hapmap]
rs1670545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1670546	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs1670558	0.98[ASN][1000 genomes]
rs1792199	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3018335	0.94[ASN][1000 genomes]
rs4362170	0.98[ASN][1000 genomes]
rs7105293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10898950	PAAF1	cis	cerebellum	SCAN
rs10898950	C11orf59	cis	parietal	SCAN
rs10898950	FLJ11848	cis	multi-tissue	Pritchard
rs10898950	WDR71	cis	multi-tissue	Pritchard
rs10898950	PPA1	trans	cerebellum	SCAN
rs10898950	OMP	cis	parietal	SCAN
rs10898950	PAAF1	cis	lymphoblastoid	seeQTL
rs10898950	PAAF1	cis	parietal	SCAN
rs10898950	RNF121	cis	cerebellum	SCAN
rs10898950	MRPL48	cis	lymphoblastoid	seeQTL
rs10898950	PAAF1	cis	Lymphoblastoid	GTEx
rs10898950	MRPL48	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73588600-73610200	Weak transcription	Gastric	stomach
2	chr11:73588600-73610200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:73588600-73611200	Weak transcription	Aorta	Aorta
4	chr11:73588800-73604200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:73588800-73604800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:73588800-73606200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr11:73588800-73607000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:73588800-73610200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:73588800-73610600	Weak transcription	Spleen	Spleen
10	chr11:73588800-73610800	Weak transcription	Lung	lung
11	chr11:73588800-73610800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:73588800-73611200	Weak transcription	Right Ventricle	heart
13	chr11:73588800-73622000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:73588800-73623000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:73588800-73625200	Weak transcription	Small Intestine	intestine
16	chr11:73588800-73630000	Weak transcription	Colonic Mucosa	Colon
17	chr11:73588800-73630200	Weak transcription	HUVEC	blood vessel
18	chr11:73589000-73602600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:73589000-73606000	Weak transcription	A549	lung
20	chr11:73589000-73610000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:73589000-73610200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:73589000-73610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:73589000-73630200	Weak transcription	Fetal Brain Male	brain
24	chr11:73589200-73601200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:73589200-73601200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:73589200-73611200	Weak transcription	Brain Substantia Nigra	brain
27	chr11:73589400-73609800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:73589400-73610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:73589400-73629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:73589600-73603400	Weak transcription	Fetal Kidney	kidney
31	chr11:73590000-73610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:73590000-73611200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:73591200-73602600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:73591200-73610200	Weak transcription	Pancreas	Pancrea
35	chr11:73591400-73605600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:73591400-73610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:73591400-73610200	Weak transcription	Esophagus	oesophagus
38	chr11:73591600-73618000	Weak transcription	K562	blood
39	chr11:73594200-73603800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:73595600-73604200	Weak transcription	Thymus	Thymus
41	chr11:73595600-73610200	Weak transcription	Ovary	ovary
42	chr11:73595800-73601200	Weak transcription	Brain Germinal Matrix	brain
43	chr11:73596000-73640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr11:73597000-73601000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:73597000-73603000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:73597000-73606400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:73597200-73607200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:73597400-73604200	Strong transcription	Placenta	Placenta
49	chr11:73597400-73605400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:73597400-73605400	Strong transcription	Liver	Liver

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