Variant report

Variant	rs695046
Chromosome Location	chr11:77594354-77594355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10899399	0.87[ASN][1000 genomes]
rs10899404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237263	0.87[ASN][1000 genomes]
rs11237280	0.89[EUR][1000 genomes]
rs11237318	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237338	0.89[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs11600140	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11606549	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11607032	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11607512	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs12279880	0.88[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs12285765	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12286317	0.87[ASN][1000 genomes]
rs12292039	1.00[YRI][hapmap]
rs13377546	0.91[YRI][hapmap]
rs17752006	0.87[ASN][1000 genomes]
rs17752458	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs1783544	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1823507	1.00[YRI][hapmap]
rs2154972	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305317	0.86[GIH][hapmap];0.92[MEX][hapmap];0.91[YRI][hapmap]
rs24356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508189	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34130561	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4322421	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4344516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs484363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4945220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56218634	0.89[EUR][1000 genomes]
rs588217	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598071	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs621456	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs623173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs623907	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628668	0.81[JPT][hapmap]
rs635195	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636971	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs648601	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648896	0.82[EUR][1000 genomes]
rs650171	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs663674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667225	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs670090	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs684813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs687037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs694845	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115801	0.89[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs7122968	0.80[AMR][1000 genomes]
rs7123080	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7131359	0.87[YRI][hapmap]
rs72949616	0.89[EUR][1000 genomes]
rs72949618	0.89[EUR][1000 genomes]
rs7950873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[TSI][hapmap]
rs7951033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs947841	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630225	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers 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
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs695046	INTS4	cis	cerebellum	SCAN
rs695046	INTS4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77566200-77594600	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:77568200-77594600	Weak transcription	Fetal Kidney	kidney
4	chr11:77569000-77597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
6	chr11:77578600-77597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:77578800-77601400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:77579200-77625000	Weak transcription	HMEC	breast
9	chr11:77579800-77597800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:77580000-77597800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:77580200-77597400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:77580600-77596000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:77580800-77597800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:77581000-77597400	Weak transcription	Psoas Muscle	Psoas
15	chr11:77582000-77598000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr11:77582600-77596000	Strong transcription	Primary T cells from cord blood	blood
17	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
19	chr11:77584600-77597800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:77584800-77596400	Strong transcription	Liver	Liver
21	chr11:77584800-77597800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:77585000-77596200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:77585200-77597800	Strong transcription	Fetal Stomach	stomach
24	chr11:77585600-77597600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:77586200-77595800	Strong transcription	Brain Anterior Caudate	brain
26	chr11:77586200-77595800	Strong transcription	Dnd41	blood
27	chr11:77586200-77596000	Strong transcription	Placenta	Placenta
28	chr11:77586200-77596400	Strong transcription	Fetal Brain Female	brain
29	chr11:77586200-77597600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:77586200-77597600	Strong transcription	Lung	lung
31	chr11:77586400-77597800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:77586600-77597800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:77586600-77597800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:77586600-77597800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
36	chr11:77586800-77597400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:77586800-77597800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:77587200-77595800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:77587200-77617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:77587400-77597600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:77587600-77597800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:77587800-77603800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:77588000-77595600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:77588200-77614000	Weak transcription	Right Ventricle	heart
45	chr11:77588800-77595800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr11:77589200-77596000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:77589200-77597400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:77589200-77597800	Strong transcription	Thymus	Thymus
49	chr11:77589400-77594400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:77589400-77597800	Strong transcription	Duodenum Mucosa	Duodenum

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