Variant report

Variant	rs644616
Chromosome Location	chr11:62444798-62444799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10792355	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11231161	0.82[JPT][hapmap]
rs11231172	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231173	0.87[ASN][1000 genomes]
rs11231176	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11231181	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231182	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231183	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231184	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12291465	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364753	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364756	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637597	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1893458	0.97[ASN][1000 genomes]
rs2849030	0.86[YRI][hapmap]
rs2849031	0.86[YRI][hapmap]
rs2956993	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2956995	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2957122	0.88[ASN][1000 genomes]
rs2958236	0.88[ASN][1000 genomes]
rs3017188	0.90[ASN][1000 genomes]
rs3017666	0.82[ASN][1000 genomes]
rs3018561	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs3809079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489748	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597259	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435036	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661182	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67909703	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693698	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128852	0.81[ASN][1000 genomes]
rs71490396	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71490397	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7949030	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9736354	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
6	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
7	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs644616	CHRM1	cis	cerebellum	SCAN
rs644616	TTC9C	cis	cerebellum	SCAN
rs644616	CNIH2	cis	parietal	SCAN
rs644616	TUT1	cis	parietal	SCAN
rs644616	EML3	cis	Esophagus Mucosa	GTEx
rs644616	CDC42EP2	cis	cerebellum	SCAN
rs644616	TTC9C	cis	parietal	SCAN
rs644616	C11orf48	cis	cerebellum	SCAN
rs644616	EML3	cis	cerebellum	SCAN
rs644616	KCNK4	cis	parietal	SCAN
rs644616	DAK	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62439800-62445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62440000-62445400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:62440000-62445600	Weak transcription	Fetal Kidney	kidney
4	chr11:62440200-62445000	Weak transcription	Right Atrium	heart
5	chr11:62440200-62445600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:62440400-62444800	Weak transcription	Stomach Mucosa	stomach
7	chr11:62440400-62445000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:62440400-62445200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:62440600-62445200	Strong transcription	Brain Anterior Caudate	brain
10	chr11:62440600-62445200	Strong transcription	Fetal Stomach	stomach
11	chr11:62440600-62445400	Strong transcription	Lung	lung
12	chr11:62440800-62444800	Strong transcription	Left Ventricle	heart
13	chr11:62440800-62445000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:62440800-62445000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:62440800-62445000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:62440800-62445400	Weak transcription	Small Intestine	intestine
17	chr11:62440800-62445600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:62441000-62444800	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:62441000-62445000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:62441000-62445000	Strong transcription	Fetal Intestine Small	intestine
21	chr11:62441200-62444800	Weak transcription	HepG2	liver
22	chr11:62441200-62445000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:62441200-62445000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:62441200-62445000	Strong transcription	Fetal Intestine Large	intestine
25	chr11:62441400-62445000	Strong transcription	Brain Germinal Matrix	brain
26	chr11:62441400-62445400	Strong transcription	Thymus	Thymus
27	chr11:62441600-62445200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:62442000-62445200	Strong transcription	NH-A	brain
29	chr11:62442200-62445000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:62442200-62445000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr11:62442200-62445000	Strong transcription	A549	lung
32	chr11:62442600-62444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:62442600-62445000	Weak transcription	Fetal Brain Male	brain
34	chr11:62443000-62445200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:62443200-62445400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:62443400-62445000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:62443400-62445000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:62443400-62445200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:62443600-62444800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:62443600-62445000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:62443600-62445000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:62443600-62445000	Genic enhancers	Liver	Liver
43	chr11:62443600-62445200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:62443800-62444800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:62443800-62444800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr11:62443800-62444800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:62443800-62444800	Genic enhancers	Dnd41	blood
48	chr11:62443800-62445000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr11:62443800-62445000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:62443800-62445000	Strong transcription	Brain Hippocampus Middle	brain

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