Variant report

Variant	rs894852
Chromosome Location	chr1:211835786-211835787
allele	C/T
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	chr1:211833950-211836077	K562	blood:	n/a	n/a
2	POLR2A	chr1:211835239-211835931	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211750433..211752019-chr1:211835257..211837969,2	K562	blood:

Variant related genes	Relation type
FDPSP8	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1067248	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1067249	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1067250	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][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];0.97[ASN][1000 genomes]
rs1542140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[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];0.99[ASN][1000 genomes]
rs1764617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1822568	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587487	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2794730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701918	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs701921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs701922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785316	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs785317	0.87[ASN][1000 genomes]
rs785318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv945280	chr1:211833548-211836203	Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs894852	IRF6	cis	cerebellum	SCAN
rs894852	C1orf186	cis	parietal	SCAN
rs894852	LAMB3	cis	cerebellum	SCAN
rs894852	MAPKAPK2	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211827600-211837600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:211827600-211847600	Weak transcription	HSMM	muscle
3	chr1:211827600-211847600	Weak transcription	NHEK	skin
4	chr1:211827800-211836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:211828200-211840400	Weak transcription	Fetal Lung	lung
6	chr1:211828400-211836600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:211828600-211835800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:211828600-211835800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:211828600-211835800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:211828600-211836600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:211828600-211836600	Weak transcription	NHDF-Ad	bronchial
12	chr1:211828600-211837600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:211828600-211837800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:211828600-211837800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:211828600-211837800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:211828600-211837800	Weak transcription	Osteobl	bone
17	chr1:211828600-211840200	Weak transcription	HMEC	breast
18	chr1:211828600-211842400	Weak transcription	NHLF	lung
19	chr1:211828600-211842800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:211828600-211845600	Weak transcription	Fetal Heart	heart
21	chr1:211828600-211847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:211828600-211847600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:211828600-211847800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:211828600-211847800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:211828600-211848000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:211828600-211848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:211828800-211836600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:211828800-211836600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:211828800-211837800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:211828800-211837800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:211828800-211837800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:211828800-211839200	Weak transcription	NH-A	brain
33	chr1:211828800-211840000	Weak transcription	HUVEC	blood vessel
34	chr1:211828800-211841800	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:211828800-211847600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:211829000-211836000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:211829000-211837400	Weak transcription	Hela-S3	cervix
38	chr1:211829000-211837600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:211829000-211837800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:211829000-211838000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:211829000-211839400	Weak transcription	K562	blood
42	chr1:211829000-211842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:211829000-211847400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:211829000-211847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:211829200-211836400	Weak transcription	A549	lung
46	chr1:211829200-211840800	Weak transcription	Fetal Intestine Large	intestine
47	chr1:211829600-211836600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:211829600-211848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:211831400-211842400	Weak transcription	Fetal Stomach	stomach
50	chr1:211832200-211837800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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