Variant report

Variant	rs1800680
Chromosome Location	chr1:227075984-227075985
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	chr1:227072686..227076463-chr1:227077857..227081301,5	K562	blood:
2	chr1:227063913..227065661-chr1:227075217..227077074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12563993	1.00[YRI][hapmap]
rs17391089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1800680	C1orf95	cis	cerebellum	SCAN
rs1800680	ITPKB	cis	parietal	SCAN
rs1800680	TMEM63A	cis	cerebellum	SCAN
rs1800680	HIST3H2BB	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
3	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
4	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
6	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:227069400-227087800	Weak transcription	HMEC	breast
12	chr1:227069400-227102800	Weak transcription	K562	blood
13	chr1:227070000-227076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:227070400-227079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
17	chr1:227071000-227076000	Weak transcription	NHEK	skin
18	chr1:227071000-227077400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:227071200-227076000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
22	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
23	chr1:227071200-227091400	Weak transcription	Osteobl	bone
24	chr1:227071400-227076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:227071400-227079000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:227071400-227079600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:227071400-227080000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
29	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:227071800-227078000	Weak transcription	NHLF	lung
31	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
32	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
34	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
35	chr1:227072800-227077800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227073000-227078800	Strong transcription	HSMMtube	muscle
38	chr1:227073000-227080400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:227073200-227076200	Weak transcription	A549	lung
41	chr1:227073200-227079600	Weak transcription	Thymus	Thymus
42	chr1:227073400-227076400	Weak transcription	Aorta	Aorta
43	chr1:227073400-227076400	Weak transcription	Esophagus	oesophagus
44	chr1:227073400-227084400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:227073400-227084600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
47	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
48	chr1:227073800-227076600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:227074200-227080400	Strong transcription	Brain Anterior Caudate	brain

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