Variant report

Variant	rs855865
Chromosome Location	chr1:159028378-159028379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:159028186-159028428	U87	brain:	n/a	n/a
2	POLR2A	chr1:159028339-159028923	U87	brain:	n/a	n/a
3	POLR2A	chr1:159028307-159028952	U87	brain:	n/a	n/a
4	POLR2A	chr1:159028129-159028525	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:159028172-159028603	U87	brain:	n/a	n/a
6	POLR2A	chr1:159019870-159029996	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:159020046-159029918	GM12891	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AIM2-2	chr1:159028176-159029238	NONHSAT006994

Variant related genes	Relation type
ENSG00000265589	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1057027	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1057028	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1101991	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1101993	0.82[CEU][hapmap]
rs1101995	0.81[CEU][hapmap]
rs1101998	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs11265132	0.82[EUR][1000 genomes]
rs11265133	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11265134	0.83[ASN][1000 genomes]
rs12090965	0.82[EUR][1000 genomes]
rs12093523	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12094545	0.82[EUR][1000 genomes]
rs12094692	0.82[EUR][1000 genomes]
rs12094741	0.82[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs12094786	0.82[EUR][1000 genomes]
rs12098223	0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12124059	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144575	0.82[EUR][1000 genomes]
rs12239136	0.82[EUR][1000 genomes]
rs12240111	0.82[EUR][1000 genomes]
rs1417804	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1614182	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1633256	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1633262	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1633265	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16841642	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1772405	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1772407	0.81[TSI][hapmap]
rs1772408	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1772414	1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1772415	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1935067	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2106094	0.82[EUR][1000 genomes]
rs2106095	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2157694	0.82[EUR][1000 genomes]
rs2157695	0.82[EUR][1000 genomes]
rs2236584	0.87[ASN][1000 genomes]
rs2298803	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2518553	0.88[EUR][1000 genomes]
rs2518555	0.87[ASN][1000 genomes]
rs2518562	0.94[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap]
rs2570916	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap]
rs2793844	0.87[ASN][1000 genomes]
rs2793845	0.97[ASN][1000 genomes]
rs2814770	0.90[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2814771	0.95[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs2840312	0.82[EUR][1000 genomes]
rs2852695	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs2852696	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs3018316	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3737522	0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs3754460	0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs3768513	0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3768514	0.84[ASN][1000 genomes]
rs3768515	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3768519	0.84[ASN][1000 genomes]
rs3768523	0.83[ASN][1000 genomes]
rs41264457	0.84[ASN][1000 genomes]
rs55719948	0.83[ASN][1000 genomes]
rs55791394	0.83[ASN][1000 genomes]
rs56235865	0.82[EUR][1000 genomes]
rs56374780	0.82[EUR][1000 genomes]
rs60958912	0.82[EUR][1000 genomes]
rs66831955	0.82[EUR][1000 genomes]
rs67772786	0.82[EUR][1000 genomes]
rs67843408	0.82[EUR][1000 genomes]
rs6940	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs73021886	0.82[EUR][1000 genomes]
rs74122232	0.84[ASN][1000 genomes]
rs7532207	0.87[ASN][1000 genomes]
rs7535630	0.82[EUR][1000 genomes]
rs7535856	0.85[GIH][hapmap]
rs7538035	0.82[EUR][1000 genomes]
rs7545770	0.82[EUR][1000 genomes]
rs855866	0.83[CEU][hapmap]
rs855871	0.83[GIH][hapmap]
rs856051	0.81[EUR][1000 genomes]
rs856052	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs856053	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs856054	0.91[CEU][hapmap]
rs856055	0.93[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs856056	0.88[EUR][1000 genomes]
rs856057	0.88[EUR][1000 genomes]
rs856058	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs861318	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs855865	AIM2	cis	lymphoblastoid	seeQTL
rs855865	IFI16	cis	cerebellum	SCAN
rs855865	IFI16	cis	parietal	SCAN
rs855865	FCRL4	cis	cerebellum	SCAN
rs855865	TMEM79	cis	parietal	SCAN
rs855865	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
2	chr1:159001400-159036200	Weak transcription	Small Intestine	intestine
3	chr1:159001600-159028400	Strong transcription	Fetal Thymus	thymus
4	chr1:159009200-159030400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:159021200-159028400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:159022400-159028800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:159022600-159031600	Weak transcription	Fetal Brain Male	brain
8	chr1:159022800-159029600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:159022800-159037400	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr1:159024200-159028600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:159024200-159032400	Weak transcription	Brain Germinal Matrix	brain
12	chr1:159024400-159028800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:159024400-159030800	Weak transcription	Placenta	Placenta
14	chr1:159025200-159037600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:159025200-159038200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:159025400-159029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:159025400-159037400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:159025400-159037800	Weak transcription	NHDF-Ad	bronchial
19	chr1:159025400-159038200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:159025600-159036400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:159025800-159029200	Weak transcription	HSMM	muscle
22	chr1:159026000-159028800	Weak transcription	Osteobl	bone
23	chr1:159026000-159030200	Weak transcription	HUVEC	blood vessel
24	chr1:159026000-159037200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:159026200-159028600	Weak transcription	Fetal Intestine Large	intestine
26	chr1:159026200-159028600	Weak transcription	HSMMtube	muscle
27	chr1:159026200-159036400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:159026200-159037200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:159026200-159037200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:159026200-159037600	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:159026200-159037600	Weak transcription	NHEK	skin
32	chr1:159026200-159037800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:159026200-159038000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:159026200-159038600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:159026400-159034000	Weak transcription	NHLF	lung
36	chr1:159026400-159034200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:159026400-159037000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:159026400-159037200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:159026400-159037200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:159026400-159037200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:159026400-159037400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:159026400-159037600	Weak transcription	Dnd41	blood
43	chr1:159026800-159028600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:159026800-159028600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:159026800-159037200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:159026800-159038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:159027000-159028600	Weak transcription	Fetal Stomach	stomach
48	chr1:159027000-159029600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:159027000-159030000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:159027000-159031800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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