Variant report

Variant	rs3768376
Chromosome Location	chr1:226845724-226845725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226845713..226848053-chr1:226861534..226863406,2	K562	blood:
2	chr1:226844059..226846179-chr1:226852486..226853988,2	K562	blood:
3	chr1:226844931..226846433-chr1:226894353..226896487,2	MCF-7	breast:
4	chr1:226838115..226840553-chr1:226843836..226846958,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10495246	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1144838	0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1144839	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs1144840	0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1151804	0.80[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1288936	0.92[JPT][hapmap]
rs17522524	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17588687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820635	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3820637	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs697843	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768376	HIST3H2BB	cis	cerebellum	SCAN
rs3768376	PARP1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226836400-226847200	Weak transcription	Ovary	ovary
2	chr1:226836800-226856200	Enhancers	Left Ventricle	heart
3	chr1:226837000-226849800	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr1:226837200-226846000	Enhancers	Brain Anterior Caudate	brain
5	chr1:226837400-226848600	Enhancers	Right Atrium	heart
6	chr1:226837400-226856200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:226837400-226856600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:226837400-226856600	Enhancers	Brain Substantia Nigra	brain
9	chr1:226838800-226848200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr1:226839200-226846800	Enhancers	Spleen	Spleen
11	chr1:226839400-226856200	Enhancers	Fetal Muscle Leg	muscle
12	chr1:226840000-226846200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:226840400-226846000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:226840600-226851800	Enhancers	Adipose Nuclei	Adipose
15	chr1:226840600-226852600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:226840600-226852800	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:226841000-226845800	Enhancers	Fetal Lung	lung
18	chr1:226841000-226847000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:226841000-226847000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:226841000-226847200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:226841200-226845800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:226841200-226845800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:226841200-226846400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:226841400-226846400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:226841400-226846400	Enhancers	Fetal Intestine Large	intestine
26	chr1:226841400-226847200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:226841800-226850200	Enhancers	Psoas Muscle	Psoas
28	chr1:226841800-226856200	Enhancers	Brain Angular Gyrus	brain
29	chr1:226841800-226860600	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:226842000-226848800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:226842200-226849200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:226842200-226850600	Enhancers	Pancreas	Pancrea
33	chr1:226842200-226852400	Enhancers	Esophagus	oesophagus
34	chr1:226842400-226846400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:226842400-226846600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:226842600-226846400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:226842800-226848000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:226843200-226850200	Genic enhancers	Fetal Thymus	thymus
39	chr1:226843400-226846000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:226843400-226846000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:226843400-226848800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:226843400-226849800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:226843400-226850400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:226843400-226850400	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr1:226843600-226846400	Enhancers	Small Intestine	intestine
46	chr1:226843600-226847200	Enhancers	Stomach Mucosa	stomach
47	chr1:226843600-226847400	Weak transcription	Liver	Liver
48	chr1:226843600-226848200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:226843600-226848400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:226843600-226849000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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