Variant report

Variant	rs12635736
Chromosome Location	chr3:42784630-42784631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42695515..42699385-chr3:42783891..42785921,3	K562	blood:
2	chr3:42713506..42715721-chr3:42783952..42785579,2	K562	blood:

Variant related genes	Relation type
ENSG00000230084	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];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865922	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]
rs11718476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11922251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11929390	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12054446	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487729	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491179	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12633707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12639142	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs13070345	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];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240859	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];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs339731	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34549959	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846063	0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs3895740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3907218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3912104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3916334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60706321	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6807878	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7639170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9839430	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs12635736	HHATL	cis	cerebellum	SCAN
rs12635736	HHATL	cis	parietal	SCAN
rs12635736	ZNF35	cis	cerebellum	SCAN
rs12635736	LRRC2	cis	cerebellum	SCAN

Chromatin state (count:27 , 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	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:42781200-42784800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:42781200-42787400	Weak transcription	Aorta	Aorta
10	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:42781600-42787400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:42782400-42785400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:42782400-42787400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:42782600-42785200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:42782600-42785400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:42783600-42785200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:42783600-42785200	Weak transcription	Right Atrium	heart
19	chr3:42783600-42785400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42783600-42786400	Weak transcription	Psoas Muscle	Psoas
21	chr3:42783800-42785200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:42783800-42785400	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:42783800-42785600	Weak transcription	Fetal Heart	heart
24	chr3:42783800-42785800	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:42784000-42785400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:42784000-42785600	Weak transcription	HepG2	liver
27	chr3:42784600-42787400	Weak transcription	Left Ventricle	heart

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