Variant report

Variant	rs2016942
Chromosome Location	chr11:8938787-8938788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8931316..8934225-chr11:8937249..8940014,3	K562	blood:
2	chr11:8932851..8934873-chr11:8937588..8939434,2	K562	blood:
3	chr11:8714148..8716877-chr11:8938589..8940698,2	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000254665	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10743095	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743096	0.82[ASN][1000 genomes]
rs10769967	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs10769968	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10769970	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769971	0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769973	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10769980	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10769981	0.81[EUR][1000 genomes]
rs10840130	0.84[CEU][hapmap]
rs10840134	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10840141	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840142	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840147	0.89[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840148	1.00[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10840157	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10840160	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs11042078	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs11042102	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042103	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042125	0.89[ASW][hapmap];0.81[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];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042149	0.89[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs11042151	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap]
rs11042152	0.85[EUR][1000 genomes]
rs11042154	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1109305	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1123936	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.91[CEU][hapmap]
rs1560569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569408	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1883098	0.86[EUR][1000 genomes]
rs1980428	0.93[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs1980429	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1984791	0.85[JPT][hapmap];0.82[MEX][hapmap]
rs1988708	0.83[EUR][1000 genomes]
rs1988709	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2012696	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2568043	0.92[CEU][hapmap]
rs2568045	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs2568054	0.83[EUR][1000 genomes]
rs2568059	0.85[EUR][1000 genomes]
rs2568061	0.93[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2568062	0.86[EUR][1000 genomes]
rs2568065	0.93[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2568090	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs2653567	0.86[EUR][1000 genomes]
rs2653570	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap]
rs2653593	0.84[EUR][1000 genomes]
rs2653605	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap]
rs2653616	0.85[EUR][1000 genomes]
rs2742471	0.85[EUR][1000 genomes]
rs2742474	0.84[EUR][1000 genomes]
rs2742480	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2742537	0.83[CEU][hapmap]
rs2742540	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742550	0.84[EUR][1000 genomes]
rs2742552	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs34842234	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4909952	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910062	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs4910119	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4910156	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910157	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910158	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910200	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910442	0.91[CEU][hapmap]
rs4929922	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486060	0.92[CEU][hapmap]
rs7119939	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7123429	0.93[CEU][hapmap]
rs7123861	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7479407	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7484180	0.86[EUR][1000 genomes]
rs7925728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7930026	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7937298	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7945705	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers 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 target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2016942	AKIP1	cis	Thyroid	GTEx
rs2016942	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2016942	C11orf17	cis	multi-tissue	Pritchard
rs2016942	RRP8	cis	parietal	SCAN
rs2016942	OR51Q1	cis	parietal	SCAN
rs2016942	WEE1	cis	parietal	SCAN
rs2016942	NRIP3	cis	parietal	SCAN
rs2016942	TMEM9B-AS1	cis	lung	GTEx
rs2016942	TMEM9B	cis	parietal	SCAN
rs2016942	TRIM22	cis	parietal	SCAN
rs2016942	CYB5R2	cis	parietal	SCAN
rs2016942	MMP26	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
4	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8934200-8941600	Weak transcription	Esophagus	oesophagus
6	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:8934800-8939400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:8935000-8940400	Genic enhancers	Fetal Muscle Leg	muscle
9	chr11:8935800-8940000	Weak transcription	Gastric	stomach
10	chr11:8936000-8939600	Weak transcription	Fetal Brain Male	brain
11	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:8936200-8939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:8936400-8938800	Weak transcription	Primary B cells from cord blood	blood
15	chr11:8936400-8938800	Weak transcription	Aorta	Aorta
16	chr11:8936400-8941800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
20	chr11:8936600-8939000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:8936600-8940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:8936600-8940800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:8936600-8941400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr11:8936600-8941600	Weak transcription	Ovary	ovary
25	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
27	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
29	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
30	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:8936800-8939200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:8936800-8940000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:8936800-8942200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:8936800-8947000	Strong transcription	Dnd41	blood
35	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
38	chr11:8937200-8945000	Strong transcription	Brain Angular Gyrus	brain
39	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
40	chr11:8937600-8944800	Strong transcription	Hela-S3	cervix
41	chr11:8937800-8939200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr11:8937800-8939800	Genic enhancers	HMEC	breast
43	chr11:8937800-8940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr11:8937800-8940800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:8938000-8938800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:8938000-8938800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:8938000-8938800	Strong transcription	Adipose Nuclei	Adipose
49	chr11:8938000-8938800	Genic enhancers	Osteobl	bone
50	chr11:8938000-8939000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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