Variant report

Variant	rs1043641
Chromosome Location	chr1:226332993-226332994
allele	A/G
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	chr1:226332428-226336021	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226324101..226327623-chr1:226332265..226334492,3	K562	blood:
2	chr1:226325163..226327819-chr1:226330574..226333396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234478	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495243	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915943	1.00[YRI][hapmap]
rs12402078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56381945	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58322813	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58416350	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66520928	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66527714	0.92[AFR][1000 genomes]
rs67431141	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67696165	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72759068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72759069	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72759091	0.87[AFR][1000 genomes]
rs72759098	0.87[EUR][1000 genomes]
rs9659809	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662238	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9725713	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9727021	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9727329	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1043641	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs1043641	PARP1	cis	cerebellum	SCAN
rs1043641	FBXO28	cis	cerebellum	SCAN
rs1043641	DEGS1	cis	parietal	SCAN
rs1043641	C1orf58	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226320800-226334000	Weak transcription	K562	blood
3	chr1:226321400-226333800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:226321400-226333800	Weak transcription	GM12878-XiMat	blood
5	chr1:226322000-226334400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:226322800-226333000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:226323200-226333200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:226323200-226333600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:226323200-226333800	Weak transcription	A549	lung
10	chr1:226323200-226334400	Weak transcription	NHEK	skin
11	chr1:226323200-226344600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:226323400-226338400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:226323600-226333800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:226323600-226333800	Weak transcription	Esophagus	oesophagus
15	chr1:226323600-226334000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:226323600-226338400	Weak transcription	Fetal Kidney	kidney
17	chr1:226323600-226339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:226323600-226339800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:226323600-226346000	Weak transcription	Fetal Heart	heart
20	chr1:226323800-226333600	Weak transcription	Fetal Intestine Large	intestine
21	chr1:226323800-226333800	Weak transcription	Ovary	ovary
22	chr1:226323800-226333800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:226323800-226334000	Weak transcription	Right Ventricle	heart
24	chr1:226323800-226338600	Weak transcription	Fetal Brain Male	brain
25	chr1:226323800-226355000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:226324000-226333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:226324000-226339800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:226324000-226340000	Weak transcription	Stomach Mucosa	stomach
29	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:226324200-226333000	Weak transcription	Colonic Mucosa	Colon
31	chr1:226324400-226334000	Weak transcription	Lung	lung
32	chr1:226324400-226334000	Weak transcription	Thymus	Thymus
33	chr1:226324400-226339800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:226324400-226346200	Weak transcription	Pancreas	Pancrea
35	chr1:226324800-226334200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:226325800-226333800	Weak transcription	Aorta	Aorta
37	chr1:226328600-226333600	Weak transcription	Brain Germinal Matrix	brain
38	chr1:226329600-226333400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:226329600-226334000	Weak transcription	NHLF	lung
40	chr1:226329600-226353800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:226329800-226333200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:226329800-226333600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:226329800-226334000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:226330000-226333600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:226330000-226341000	Weak transcription	Psoas Muscle	Psoas
46	chr1:226330600-226334000	Weak transcription	Brain Anterior Caudate	brain
47	chr1:226330600-226354200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:226330800-226334800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:226330800-226336800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:226330800-226337400	Strong transcription	Primary B cells from peripheral blood	blood

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