Variant report

Variant	rs10865922
Chromosome Location	chr3:42781532-42781533
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42781201..42784093-chr3:42790186..42792951,2	K562	blood:
2	chr3:42777883..42779575-chr3:42780647..42782304,2	K562	blood:
3	chr3:42779798..42781927-chr3:42890891..42893467,2	K562	blood:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10490794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487729	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12491179	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12633707	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12635736	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639142	0.87[CHB][hapmap]
rs13070345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240859	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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs339731	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34549959	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846063	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3895740	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3907218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912104	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3916334	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60706321	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6807878	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639483	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9830553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9839430	0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10865922	ZNF35	cis	cerebellum	SCAN
rs10865922	HHATL	cis	cerebellum	SCAN
rs10865922	LRRC2	cis	cerebellum	SCAN
rs10865922	HHATL	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:42769800-42787600	Weak transcription	Gastric	stomach
3	chr3:42776800-42787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
5	chr3:42778200-42788000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:42778400-42786400	Weak transcription	Right Ventricle	heart
7	chr3:42780400-42782600	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:42780600-42781800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:42780600-42781800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:42780600-42782000	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:42780600-42782200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:42780600-42782400	Enhancers	Brain Angular Gyrus	brain
13	chr3:42780600-42782600	Enhancers	Brain Anterior Caudate	brain
14	chr3:42780600-42783600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42780600-42783800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:42780600-42783800	Enhancers	Brain Substantia Nigra	brain
17	chr3:42780800-42781600	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:42780800-42781800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:42780800-42783600	Enhancers	Psoas Muscle	Psoas
20	chr3:42780800-42783800	Enhancers	Fetal Muscle Leg	muscle
21	chr3:42781000-42781600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:42781000-42781600	Enhancers	Lung	lung
23	chr3:42781000-42781600	Enhancers	HSMMtube	muscle
24	chr3:42781000-42782000	Enhancers	HepG2	liver
25	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:42781200-42781600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:42781200-42782200	Weak transcription	Left Ventricle	heart
28	chr3:42781200-42782400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:42781200-42783800	Enhancers	Fetal Heart	heart
30	chr3:42781200-42784800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:42781200-42787400	Weak transcription	Aorta	Aorta
32	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:42781400-42781600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:42781400-42783600	Enhancers	Right Atrium	heart

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