Variant report

Variant	rs11144476
Chromosome Location	chr9:71566847-71566848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10114061	0.91[ASN][1000 genomes]
rs10114872	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs10115104	0.91[ASN][1000 genomes]
rs10115155	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115608	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10117043	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10117188	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10117198	0.83[GIH][hapmap]
rs10122975	0.89[ASN][1000 genomes]
rs10124169	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10746973	0.86[GIH][hapmap]
rs10746974	0.89[GIH][hapmap]
rs10746979	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10781264	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs10781283	0.90[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10781293	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869487	0.81[CEU][hapmap]
rs10869541	0.81[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs10869543	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10869572	0.93[ASN][1000 genomes]
rs10869574	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869578	0.92[ASN][1000 genomes]
rs10869599	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10869607	0.99[ASN][1000 genomes]
rs10869610	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11143802	0.94[CEU][hapmap]
rs11144468	0.92[GIH][hapmap]
rs12337140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12349586	0.94[CEU][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap]
rs12352694	0.89[AMR][1000 genomes]
rs12379823	0.81[GIH][hapmap]
rs13300006	0.88[ASN][1000 genomes]
rs2027205	0.85[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2152649	0.85[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.86[ASN][1000 genomes]
rs2309384	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4375069	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4745402	0.83[JPT][hapmap]
rs4745451	0.95[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap]
rs6560420	1.00[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs6560444	0.90[CEU][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6560467	0.91[ASN][1000 genomes]
rs7018692	0.90[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs7020192	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021212	0.85[CEU][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7031059	0.95[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap]
rs7037010	0.95[ASN][1000 genomes]
rs7041792	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs756326	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7852633	0.94[CEU][hapmap]
rs7853501	0.81[CEU][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7867240	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7873239	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
19	esv1833433	chr9:71544920-71598165	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11144476	FAM108B1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
2	chr9:71519400-71573000	Weak transcription	Gastric	stomach
3	chr9:71535000-71569600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:71549200-71570000	Weak transcription	Fetal Stomach	stomach
5	chr9:71549600-71569600	Weak transcription	Fetal Kidney	kidney
6	chr9:71553400-71567200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:71554400-71569600	Weak transcription	Aorta	Aorta
8	chr9:71557600-71578400	Weak transcription	HepG2	liver
9	chr9:71558000-71569200	Weak transcription	Right Ventricle	heart
10	chr9:71558200-71579200	Weak transcription	Colonic Mucosa	Colon
11	chr9:71562400-71578000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:71562400-71579400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:71563400-71567000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:71563400-71569600	Weak transcription	Brain Germinal Matrix	brain
15	chr9:71563400-71569600	Weak transcription	Spleen	Spleen
16	chr9:71563400-71578400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:71564000-71567000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr9:71564400-71567200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:71564400-71567400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:71564600-71570000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:71565000-71569600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:71565200-71569000	Enhancers	Small Intestine	intestine
23	chr9:71565200-71569600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:71565600-71569200	Weak transcription	Fetal Intestine Large	intestine
25	chr9:71565600-71569800	Weak transcription	Left Ventricle	heart
26	chr9:71565600-71587800	Weak transcription	Lung	lung
27	chr9:71565800-71576200	Weak transcription	Fetal Heart	heart
28	chr9:71566200-71568600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr9:71566400-71567400	Genic enhancers	Primary B cells from cord blood	blood
30	chr9:71566400-71567400	Enhancers	Primary B cells from peripheral blood	blood
31	chr9:71566400-71567800	Enhancers	Primary hematopoietic stem cells	blood
32	chr9:71566400-71571600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:71566600-71567600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:71566600-71568600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr9:71566600-71569400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:71566600-71571000	Weak transcription	Fetal Intestine Small	intestine
37	chr9:71566800-71567400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:71566800-71567400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:71566800-71567400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr9:71566800-71567400	Flanking Active TSS	GM12878-XiMat	blood
41	chr9:71566800-71567600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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