Variant report

Variant	rs10493773
Chromosome Location	chr1:86125753-86125754
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	chr1:86046915..86048660-chr1:86125105..86127128,2	K562	blood:
2	chr1:86125056..86127073-chr1:86141967..86144590,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL24A1-1	chr1:86124367-86126130	ENSG00000249070

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10158408	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10493774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161649	0.88[CEU][hapmap]
rs12061951	0.84[YRI][hapmap]
rs12067749	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12075929	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs12564080	0.88[CEU][hapmap]
rs12722770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739713	0.88[CEU][hapmap]
rs12751296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12754358	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17394091	0.82[AFR][1000 genomes]
rs17398175	1.00[ASW][hapmap];0.94[CHD][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17398321	0.84[ASN][1000 genomes]
rs2069208	0.88[CEU][hapmap]
rs2274738	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34746573	0.82[AFR][1000 genomes]
rs3767163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414618	0.81[CEU][hapmap]
rs55654440	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576784	0.88[CEU][hapmap]
rs6667672	0.83[AMR][1000 genomes]
rs6697548	0.87[AMR][1000 genomes]
rs6698578	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7354850	0.85[ASN][1000 genomes]
rs7523292	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10493773	LOC339524	cis	parietal	SCAN
rs10493773	DNASE2B	cis	cerebellum	SCAN
rs10493773	ZNHIT6	cis	lymphoblastoid	seeQTL
rs10493773	C1orf52	cis	cerebellum	SCAN
rs10493773	ZNHIT6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
3	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
4	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:86103600-86172600	Weak transcription	Gastric	stomach
10	chr1:86106000-86141200	Weak transcription	Lung	lung
11	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
15	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
16	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:86116400-86127000	Weak transcription	Fetal Kidney	kidney
19	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:86116600-86129200	Weak transcription	Aorta	Aorta
22	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
24	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
25	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
26	chr1:86119200-86133000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:86119200-86142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:86119200-86142200	Weak transcription	Placenta	Placenta
29	chr1:86119400-86125800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:86119400-86128800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:86119400-86134000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:86119400-86135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:86119400-86140600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:86119400-86140800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:86119400-86142200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:86119400-86142200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:86119400-86143400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:86119600-86138800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:86119600-86140600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:86119600-86142200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:86119600-86157800	Weak transcription	Hela-S3	cervix
42	chr1:86119600-86172000	Weak transcription	Colonic Mucosa	Colon
43	chr1:86119800-86129200	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:86119800-86134000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:86119800-86139600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:86119800-86171800	Weak transcription	Fetal Brain Male	brain
47	chr1:86120000-86125800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:86120000-86129600	Weak transcription	Fetal Intestine Large	intestine
49	chr1:86120000-86134600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:86120000-86135200	Weak transcription	Ovary	ovary

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