Variant report

Variant	rs12043009
Chromosome Location	chr1:153234295-153234296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10159119	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10494292	0.83[CEU][hapmap]
rs10494293	0.83[CEU][hapmap]
rs10494294	0.83[CEU][hapmap]
rs10494295	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10494296	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10494297	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788862	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10888537	0.83[CEU][hapmap]
rs10888538	0.83[CEU][hapmap]
rs10888539	0.83[CEU][hapmap]
rs11205222	0.83[CEU][hapmap]
rs11205223	0.83[CEU][hapmap]
rs11205225	0.83[CEU][hapmap]
rs11205227	0.83[CEU][hapmap]
rs11205228	0.88[CEU][hapmap]
rs11205229	0.80[CEU][hapmap]
rs11205231	0.87[CEU][hapmap]
rs11205232	0.81[EUR][1000 genomes]
rs11205238	0.82[EUR][1000 genomes]
rs11205248	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11205251	0.83[LWK][hapmap];0.86[YRI][hapmap]
rs11205252	0.86[YRI][hapmap]
rs1143390	0.89[LWK][hapmap];0.96[YRI][hapmap]
rs11583156	0.81[EUR][1000 genomes]
rs11583609	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11589914	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069007	0.83[CEU][hapmap]
rs12122588	0.83[EUR][1000 genomes]
rs12127862	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12134915	0.83[EUR][1000 genomes]
rs12136409	0.82[EUR][1000 genomes]
rs12142970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12747804	0.82[EUR][1000 genomes]
rs12760683	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329099	0.82[EUR][1000 genomes]
rs1329100	0.82[EUR][1000 genomes]
rs1410859	0.83[CEU][hapmap]
rs16835073	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs16835081	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs16835083	0.82[EUR][1000 genomes]
rs16835093	0.83[CEU][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs2094638	0.86[YRI][hapmap]
rs34119886	0.82[EUR][1000 genomes]
rs35358388	0.82[EUR][1000 genomes]
rs71626758	0.82[EUR][1000 genomes]
rs7538295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs873234	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003014	chr1:153209833-153263691	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv535172	chr1:153209833-153263691	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv998032	chr1:153210770-153264131	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3397000	chr1:153232553-153235701	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3492670	chr1:153232803-153235301	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3492671	chr1:153232803-153235301	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12043009	HIST2H2AC	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153233200-153234400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr1:153233200-153234400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr1:153233200-153234400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
4	chr1:153233200-153234400	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr1:153233200-153234600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:153233200-153234600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr1:153233200-153234600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:153233200-153234600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:153233200-153234600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:153233200-153234600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:153233200-153234800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:153233200-153234800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:153233200-153235000	Enhancers	Spleen	Spleen
14	chr1:153233400-153234400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:153233400-153234400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:153233400-153234400	Active TSS	Brain Germinal Matrix	brain
17	chr1:153233400-153234600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:153233400-153235000	Flanking Bivalent TSS/Enh	HMEC	breast
19	chr1:153233600-153234400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:153233600-153234400	Bivalent/Poised TSS	Thymus	Thymus
21	chr1:153233600-153234600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:153233600-153234600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:153233600-153234600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:153233600-153234600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:153233800-153234400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:153233800-153234400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:153233800-153234400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:153233800-153234400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:153233800-153234400	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr1:153233800-153234400	Active TSS	Brain Anterior Caudate	brain
31	chr1:153233800-153234400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:153233800-153234400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:153233800-153234400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
34	chr1:153233800-153234400	Bivalent/Poised TSS	HUVEC	blood vessel
35	chr1:153233800-153234400	Bivalent/Poised TSS	NH-A	brain
36	chr1:153233800-153234400	Bivalent/Poised TSS	NHEK	skin
37	chr1:153233800-153234600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:153233800-153234600	Active TSS	Esophagus	oesophagus
39	chr1:153233800-153234800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:153233800-153234800	Bivalent/Poised TSS	A549	lung
41	chr1:153233800-153235000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:153234000-153234400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr1:153234000-153234400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:153234000-153234400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
45	chr1:153234000-153234400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:153234000-153234400	Bivalent Enhancer	Liver	Liver
47	chr1:153234000-153234400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr1:153234000-153234400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
49	chr1:153234000-153234400	Flanking Active TSS	Gastric	stomach
50	chr1:153234000-153234400	Flanking Bivalent TSS/Enh	Left Ventricle	heart

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