Variant report

Variant	rs11744817
Chromosome Location	chr5:112427019-112427020
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112426783..112429222-chr5:112432202..112433708,2	K562	blood:
2	chr5:112426149..112427047-chr5:112665549..112666859,5	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10036854	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10045658	0.84[CHB][hapmap]
rs10058407	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs10077067	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10223151	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs10223152	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs11241190	0.84[CHB][hapmap]
rs11744218	0.84[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs11744828	0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11744956	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs11750093	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs11960706	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12513669	0.81[ASN][1000 genomes]
rs13174818	0.81[ASN][1000 genomes]
rs2227950	0.81[ASN][1000 genomes]
rs28535973	0.97[ASN][1000 genomes]
rs28620751	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28774401	0.81[ASN][1000 genomes]
rs3890775	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs3890776	0.81[ASN][1000 genomes]
rs4283779	0.84[CHB][hapmap]
rs4397121	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs4645326	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs4705539	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs56054154	0.81[ASN][1000 genomes]
rs6594675	0.80[ASN][1000 genomes]
rs6594679	0.81[ASN][1000 genomes]
rs6594680	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6859562	0.90[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859813	0.82[ASN][1000 genomes]
rs6861166	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs6861336	1.00[CEU][hapmap];0.80[MKK][hapmap]
rs6865585	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865804	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6866442	0.81[ASN][1000 genomes]
rs6866566	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs6866706	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6866718	0.81[ASN][1000 genomes]
rs6873623	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6874230	0.86[MEX][hapmap]
rs6878846	0.81[ASN][1000 genomes]
rs6879138	0.84[CHB][hapmap]
rs6879633	0.85[CHD][hapmap]
rs6879634	0.81[ASN][1000 genomes]
rs6879942	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs6882155	1.00[CEU][hapmap]
rs6882309	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6882689	0.81[ASN][1000 genomes]
rs6888031	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6888485	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6890833	0.90[CEU][hapmap]
rs6894700	0.80[ASN][1000 genomes]
rs6898297	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs7713290	0.83[CHB][hapmap]
rs7713336	0.84[CHB][hapmap]
rs7714010	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs7714160	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7714275	0.81[ASN][1000 genomes]
rs7714334	0.81[ASN][1000 genomes]
rs7714349	0.81[ASN][1000 genomes]
rs7714363	0.80[ASN][1000 genomes]
rs7714492	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7714725	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7728858	0.81[ASN][1000 genomes]
rs7728921	0.81[ASN][1000 genomes]
rs7732048	0.80[ASN][1000 genomes]
rs7734411	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7734511	0.81[ASN][1000 genomes]
rs7736823	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs7737329	0.81[ASN][1000 genomes]
rs9326874	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs9326875	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11744817	MCC	cis	cerebellum	SCAN
rs11744817	AQPEP	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112391600-112439000	Weak transcription	Gastric	stomach
3	chr5:112399000-112432800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:112404400-112428000	Weak transcription	Placenta	Placenta
6	chr5:112404400-112436800	Weak transcription	Fetal Brain Male	brain
7	chr5:112411000-112431800	Weak transcription	Spleen	Spleen
8	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:112411800-112428000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:112412000-112435200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:112412200-112432400	Weak transcription	Fetal Intestine Small	intestine
12	chr5:112417800-112436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112418600-112436600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:112419600-112436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:112420800-112436800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:112421000-112430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:112421000-112431800	Weak transcription	Pancreas	Pancrea
20	chr5:112421000-112437000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:112421000-112439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:112421400-112437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:112422200-112427800	Enhancers	Fetal Heart	heart
24	chr5:112424200-112427600	Enhancers	Psoas Muscle	Psoas
25	chr5:112424200-112435600	Weak transcription	Small Intestine	intestine
26	chr5:112424400-112428200	Enhancers	Right Atrium	heart
27	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:112425200-112428200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:112425400-112428600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:112425400-112428800	Enhancers	HMEC	breast
31	chr5:112425400-112429400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:112425600-112427200	Enhancers	Brain Germinal Matrix	brain
33	chr5:112425600-112427400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr5:112425600-112427600	Enhancers	Brain Anterior Caudate	brain
35	chr5:112425600-112428200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:112425600-112428800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:112425800-112427600	Enhancers	Brain Substantia Nigra	brain
38	chr5:112426000-112428000	Enhancers	Ovary	ovary
39	chr5:112426000-112430600	Weak transcription	NHDF-Ad	bronchial
40	chr5:112426000-112435200	Weak transcription	Adipose Nuclei	Adipose
41	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:112426200-112428400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:112426200-112437400	Weak transcription	Aorta	Aorta
44	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:112426400-112427200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr5:112426400-112427200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:112426400-112427600	Enhancers	Right Ventricle	heart
48	chr5:112426400-112428000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:112426400-112430600	Weak transcription	Osteobl	bone
50	chr5:112426600-112427200	Enhancers	Muscle Satellite Cultured Cells	--

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