Variant report

Variant	rs12402078
Chromosome Location	chr1:226355373-226355374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226348768..226351185-chr1:226353522..226355799,2	K562	blood:
2	chr1:226260259..226262161-chr1:226354959..226356498,2	K562	blood:
3	chr1:226354790..226356919-chr1:226372358..226374762,4	MCF-7	breast:
4	chr1:226338792..226340351-chr1:226353525..226355664,2	K562	blood:

Variant related genes	Relation type
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1043641	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]
rs10495243	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915943	1.00[YRI][hapmap]
rs56381945	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58322813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58416350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66520928	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66527714	0.92[AFR][1000 genomes]
rs67431141	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67696165	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759091	0.87[AFR][1000 genomes]
rs72759098	0.89[EUR][1000 genomes]
rs9659809	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9662238	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9725713	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9727021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12402078	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:226331600-226355600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:226333000-226356400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:226340400-226369600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:226347000-226369600	Weak transcription	Psoas Muscle	Psoas
6	chr1:226348800-226356000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:226348800-226365200	Weak transcription	NHEK	skin
8	chr1:226349000-226366400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:226349000-226373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:226349400-226369200	Weak transcription	Fetal Heart	heart
11	chr1:226349800-226366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:226350000-226363200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:226350000-226370200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:226350000-226373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:226350600-226363800	Weak transcription	Aorta	Aorta
16	chr1:226350600-226369000	Weak transcription	Hela-S3	cervix
17	chr1:226350800-226369600	Weak transcription	Right Ventricle	heart
18	chr1:226351000-226369800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:226351200-226360000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:226352200-226372800	Weak transcription	Fetal Kidney	kidney
21	chr1:226352400-226363200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:226352400-226365200	Weak transcription	HMEC	breast
23	chr1:226352400-226368200	Weak transcription	HSMM	muscle
24	chr1:226352600-226356000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:226352600-226356000	Weak transcription	Stomach Mucosa	stomach
26	chr1:226352600-226358400	Weak transcription	Gastric	stomach
27	chr1:226352600-226360000	Weak transcription	K562	blood
28	chr1:226352600-226360200	Weak transcription	Small Intestine	intestine
29	chr1:226352600-226360400	Weak transcription	Pancreas	Pancrea
30	chr1:226352600-226360400	Weak transcription	Spleen	Spleen
31	chr1:226352600-226365200	Weak transcription	A549	lung
32	chr1:226352600-226369200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:226352600-226370000	Weak transcription	Fetal Brain Female	brain
34	chr1:226352600-226370400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:226352600-226372200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:226352600-226372400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:226352600-226372800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:226352600-226373000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:226352600-226373400	Weak transcription	Esophagus	oesophagus
40	chr1:226352800-226365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:226352800-226372000	Weak transcription	Colonic Mucosa	Colon
42	chr1:226353000-226359800	Weak transcription	GM12878-XiMat	blood
43	chr1:226353000-226360000	Weak transcription	Lung	lung
44	chr1:226353000-226363000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:226353000-226369400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:226353000-226369600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:226353000-226370200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:226353000-226372000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:226353200-226360400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:226353200-226365000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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