Variant report

Variant	rs948394
Chromosome Location	chr12:48055232-48055233
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	chr12:48049652..48051782-chr12:48054886..48057074,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10875679	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1153975	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11609044	0.85[EUR][1000 genomes]
rs11615078	0.82[EUR][1000 genomes]
rs1232976	0.83[AMR][1000 genomes]
rs1232981	0.86[AMR][1000 genomes]
rs1232985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs1232987	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1233042	0.99[ASN][1000 genomes]
rs1233044	0.96[ASN][1000 genomes]
rs1233045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233046	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1233047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234820	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1235151	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580458	0.86[EUR][1000 genomes]
rs2022526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs2022527	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2074535	0.85[EUR][1000 genomes]
rs2155794	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2155795	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs2524317	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs2525448	0.92[AMR][1000 genomes]
rs2525449	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2847433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5006306	0.86[EUR][1000 genomes]
rs590089	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs603042	0.81[ASN][1000 genomes]
rs605026	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs611208	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs612096	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61917588	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61917615	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs622728	0.92[AMR][1000 genomes]
rs623947	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs628070	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs652457	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652543	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs652898	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs663945	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs666154	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs667610	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs681100	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs682782	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs688815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs948392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv518487	chr12:48051456-48057791	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs948394	C1QL4	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:48029400-48055400	Weak transcription	Thymus	Thymus
3	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
5	chr12:48031400-48058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48036600-48055400	Weak transcription	Ovary	ovary
7	chr12:48038200-48059400	Weak transcription	Small Intestine	intestine
8	chr12:48039400-48058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
10	chr12:48042200-48058400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:48042400-48060200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:48043400-48080000	Weak transcription	NHEK	skin
13	chr12:48043800-48055600	Weak transcription	Right Ventricle	heart
14	chr12:48045200-48059600	Weak transcription	HMEC	breast
15	chr12:48045200-48060200	Weak transcription	Spleen	Spleen
16	chr12:48045200-48079200	Weak transcription	NHLF	lung
17	chr12:48045400-48055800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:48045600-48055800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:48045600-48055800	Weak transcription	Hela-S3	cervix
20	chr12:48045600-48056600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:48045600-48062200	Weak transcription	Stomach Mucosa	stomach
22	chr12:48045800-48058200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:48045800-48058400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:48046000-48055400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:48046000-48058400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:48046200-48068000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:48046400-48061200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:48046600-48055400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:48046600-48057800	Weak transcription	Fetal Intestine Small	intestine
30	chr12:48046600-48058200	Weak transcription	Brain Substantia Nigra	brain
31	chr12:48046600-48058400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:48046600-48060000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:48046600-48060000	Weak transcription	Fetal Kidney	kidney
34	chr12:48046600-48083000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
37	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:48046600-48099200	Weak transcription	Gastric	stomach
40	chr12:48046800-48055400	Weak transcription	Liver	Liver
41	chr12:48046800-48056400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:48046800-48058200	Weak transcription	HSMMtube	muscle
43	chr12:48046800-48058400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:48046800-48058400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:48046800-48058400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:48046800-48079200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:48046800-48083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:48047000-48055400	Weak transcription	K562	blood

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