Variant report

Variant	rs11161649
Chromosome Location	chr1:86165446-86165447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86162153..86164641-chr1:86165348..86167179,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1047893	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs10493773	0.88[CEU][hapmap]
rs10493774	0.88[CEU][hapmap]
rs10873716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10873717	0.87[ASN][1000 genomes]
rs11161650	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161654	0.87[ASN][1000 genomes]
rs11161656	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161657	0.87[ASN][1000 genomes]
rs11161658	0.87[ASN][1000 genomes]
rs11161659	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11161660	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161661	0.87[ASN][1000 genomes]
rs11161662	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161663	0.87[ASN][1000 genomes]
rs11161664	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11161665	0.87[ASN][1000 genomes]
rs11161667	0.84[ASN][1000 genomes]
rs12058974	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12063702	0.84[ASN][1000 genomes]
rs12075929	0.96[CEU][hapmap]
rs12089500	0.85[ASN][1000 genomes]
rs12097932	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12564080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566746	0.87[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs12738010	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12739713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12752817	0.84[ASN][1000 genomes]
rs12754358	0.84[CEU][hapmap]
rs12756013	0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757270	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539444	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs1889919	0.87[ASN][1000 genomes]
rs1889920	0.87[ASN][1000 genomes]
rs2069208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274738	0.89[CEU][hapmap]
rs2389972	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35438778	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3753786	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs3753789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3753790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3767163	0.88[CEU][hapmap]
rs414618	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6576784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672312	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs6689168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6697535	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs6698578	0.88[CEU][hapmap]
rs7518312	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520491	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7554844	0.84[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11161649	C1orf181	cis	multi-tissue	Pritchard
rs11161649	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs11161649	ZNHIT6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
2	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:86103600-86172600	Weak transcription	Gastric	stomach
4	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
6	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
7	chr1:86119600-86172000	Weak transcription	Colonic Mucosa	Colon
8	chr1:86119800-86171800	Weak transcription	Fetal Brain Male	brain
9	chr1:86132800-86165800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:86134200-86172600	Weak transcription	Right Ventricle	heart
11	chr1:86134600-86172400	Weak transcription	Stomach Mucosa	stomach
12	chr1:86135200-86171200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:86135600-86172000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:86141600-86171800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:86142400-86170600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:86142600-86166200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:86142600-86166400	Weak transcription	Lung	lung
18	chr1:86142600-86170800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:86142600-86171000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:86142600-86172600	Weak transcription	Thymus	Thymus
21	chr1:86142600-86172600	Weak transcription	Spleen	Spleen
22	chr1:86142800-86166400	Weak transcription	Placenta	Placenta
23	chr1:86144200-86166200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:86144200-86166800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:86144200-86168200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:86144400-86165800	Weak transcription	K562	blood
27	chr1:86144400-86167600	Weak transcription	Fetal Lung	lung
28	chr1:86144400-86170400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:86146000-86166000	Weak transcription	Fetal Intestine Large	intestine
30	chr1:86146000-86170600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:86146400-86165800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:86146600-86166200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:86147000-86172600	Weak transcription	Brain Angular Gyrus	brain
34	chr1:86147200-86169400	Weak transcription	Brain Anterior Caudate	brain
35	chr1:86147200-86172000	Weak transcription	Fetal Kidney	kidney
36	chr1:86147200-86172600	Weak transcription	Psoas Muscle	Psoas
37	chr1:86147200-86172800	Weak transcription	Aorta	Aorta
38	chr1:86147600-86166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:86149000-86166000	Weak transcription	HepG2	liver
40	chr1:86154800-86166000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:86155400-86171800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:86157400-86166400	Weak transcription	Fetal Thymus	thymus
43	chr1:86157800-86172600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:86157800-86173000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:86158000-86165800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:86158000-86166200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:86158000-86166400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:86158000-86166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:86158000-86166400	Weak transcription	Fetal Stomach	stomach
50	chr1:86158000-86167400	Weak transcription	Ovary	ovary

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