Variant report

Variant	rs236894
Chromosome Location	chr1:171669823-171669824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171667939..171671943-chr1:171675100..171678672,3	K562	blood:
2	chr1:171665381..171668263-chr1:171669803..171671698,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1045456	1.00[CEU][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10489252	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10913683	0.81[EUR][1000 genomes]
rs10913684	0.81[EUR][1000 genomes]
rs12091786	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs12565176	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12567851	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12730717	0.81[EUR][1000 genomes]
rs12742601	0.82[EUR][1000 genomes]
rs12753043	0.81[EUR][1000 genomes]
rs17596025	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17596081	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs17649609	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17650310	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs17650340	0.81[EUR][1000 genomes]
rs1801898	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2143369	0.81[EUR][1000 genomes]
rs2181216	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2223602	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2232807	0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs2232813	0.81[EUR][1000 genomes]
rs2232819	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2232824	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2232825	1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs2294718	1.00[CEU][hapmap]
rs236897	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236898	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs236899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs236900	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs236907	1.00[CEU][hapmap]
rs34320898	0.82[EUR][1000 genomes]
rs34627492	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35400839	0.82[EUR][1000 genomes]
rs35631282	0.82[EUR][1000 genomes]
rs35674909	0.82[EUR][1000 genomes]
rs35882887	0.81[EUR][1000 genomes]
rs35930163	0.81[EUR][1000 genomes]
rs36080557	0.81[EUR][1000 genomes]
rs3891278	0.81[EUR][1000 genomes]
rs56365362	0.81[EUR][1000 genomes]
rs56377810	0.82[EUR][1000 genomes]
rs61807979	0.81[EUR][1000 genomes]
rs6656852	0.81[EUR][1000 genomes]
rs6674364	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6675708	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6681322	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6689125	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6695933	0.82[EUR][1000 genomes]
rs7522582	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7536142	0.81[EUR][1000 genomes]

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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs236894	METTL13	cis	cerebellum	SCAN
rs236894	RHOA	trans	parietal	SCAN
rs236894	PIGC	cis	parietal	SCAN
rs236894	C1orf9	cis	parietal	SCAN
rs236894	DUSP27	cis	parietal	SCAN
rs236894	VAMP4	cis	cerebellum	SCAN
rs236894	MAEL	cis	parietal	SCAN
rs236894	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs236894	BAT2L2	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:171666000-171674200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
13	chr1:171666200-171670800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:171666200-171676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:171666200-171682600	Weak transcription	Lung	lung
16	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
17	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
18	chr1:171666400-171673000	Weak transcription	Primary B cells from cord blood	blood
19	chr1:171666600-171676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:171666600-171686200	Weak transcription	Gastric	stomach
22	chr1:171666800-171670000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:171666800-171671800	Weak transcription	Liver	Liver
24	chr1:171666800-171673600	Weak transcription	HSMM	muscle
25	chr1:171666800-171674200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:171666800-171674200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:171666800-171675600	Weak transcription	Colonic Mucosa	Colon
28	chr1:171666800-171679200	Weak transcription	NH-A	brain
29	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:171667000-171670400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:171667000-171672600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:171667000-171672800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:171667000-171675800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:171667000-171676600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:171667000-171676800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:171667000-171685000	Weak transcription	Osteobl	bone
41	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
42	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
43	chr1:171667200-171670600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:171667200-171672800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:171667400-171670600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:171667600-171674400	Weak transcription	Placenta	Placenta
47	chr1:171667600-171676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:171667600-171681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
50	chr1:171667800-171676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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