Variant report

Variant	rs674021
Chromosome Location	chr12:121248584-121248585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121240989..121243362-chr12:121247289..121249209,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1067742	0.81[ASN][1000 genomes]
rs1105416	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11065286	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1151851	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs1168945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1168954	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1168956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1696363	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap]
rs1718211	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2454729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2649996	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2649998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2650006	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2948150	1.00[YRI][hapmap]
rs3844037	0.95[ASN][1000 genomes]
rs4767938	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs482522	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs484456	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs487310	0.89[CHB][hapmap];0.95[ASN][1000 genomes]
rs487912	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs488172	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs491602	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs493811	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs497273	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs498230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509152	0.84[ASW][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs516649	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs516978	0.83[AMR][1000 genomes]
rs520405	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs529584	0.81[CHB][hapmap]
rs532140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs532703	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs538785	0.82[ASN][1000 genomes]
rs550349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs551087	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs564120	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs566704	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs566994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs568297	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs584001	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs586305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs589699	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs594507	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs597203	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs610578	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs618849	0.81[ASN][1000 genomes]
rs619679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs620772	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs623857	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs628771	0.82[ASN][1000 genomes]
rs631168	0.82[ASN][1000 genomes]
rs633084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6553	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs656933	0.81[ASN][1000 genomes]
rs662284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662739	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs679833	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs680303	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs683437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs688402	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs694303	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs697859	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs790675	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs791210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs791707	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs791713	0.82[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs674021	P2RX4	cis	cerebellum	SCAN
rs674021	WSB2	cis	cerebellum	SCAN
rs674021	P2RX4	cis	parietal	SCAN
rs674021	UNQ1887	cis	Temporal Cortex	GTEx
rs674021	UNC119B	cis	cerebellum	SCAN
rs674021	SDC1	trans	lymphoblastoid	seeQTL
rs674021	NOS1	cis	parietal	SCAN
rs674021	SPPL3	cis	cerebellum	SCAN
rs674021	SPPL3	cis	parietal	SCAN
rs674021	ARL6IP4	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121211400-121260800	Weak transcription	Gastric	stomach
2	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:121222200-121274000	Weak transcription	Lung	lung
5	chr12:121222600-121249200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:121222600-121259000	Weak transcription	Ovary	ovary
7	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
8	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
9	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:121222800-121249400	Weak transcription	HSMM	muscle
11	chr12:121230000-121255200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:121234600-121250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:121234600-121263000	Weak transcription	A549	lung
15	chr12:121234800-121250600	Weak transcription	Fetal Brain Female	brain
16	chr12:121235000-121249600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:121236400-121259000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:121237000-121255400	Weak transcription	Fetal Heart	heart
19	chr12:121237400-121249000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:121237600-121252000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:121237600-121252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:121237800-121253200	Weak transcription	K562	blood
23	chr12:121237800-121253400	Weak transcription	Psoas Muscle	Psoas
24	chr12:121237800-121255600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:121238000-121249400	Weak transcription	HSMMtube	muscle
26	chr12:121238800-121250200	Weak transcription	NH-A	brain
27	chr12:121239000-121249000	Weak transcription	Brain Anterior Caudate	brain
28	chr12:121239200-121251000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:121239200-121252600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:121239200-121252800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:121239200-121255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:121239200-121260600	Weak transcription	Right Atrium	heart
33	chr12:121239400-121249200	Weak transcription	Brain Substantia Nigra	brain
34	chr12:121239400-121250200	Weak transcription	NHEK	skin
35	chr12:121239400-121253000	Weak transcription	Fetal Kidney	kidney
36	chr12:121239400-121255200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:121239600-121249000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:121239600-121255200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:121239800-121255200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr12:121240000-121252800	Weak transcription	Fetal Lung	lung
41	chr12:121240600-121248600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:121240800-121250400	Weak transcription	HepG2	liver
43	chr12:121240800-121260800	Weak transcription	Small Intestine	intestine
44	chr12:121241000-121252000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:121241200-121249200	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:121241200-121252000	Weak transcription	HUVEC	blood vessel
48	chr12:121241200-121258400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:121241200-121259000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:121241800-121255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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