Variant report

Variant	rs3907218
Chromosome Location	chr3:42776521-42776522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42727358..42730131-chr3:42775132..42777505,2	MCF-7	breast:
2	chr3:42681634..42683694-chr3:42776062..42778558,2	K562	blood:

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];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865922	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]
rs11718476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11922251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11929390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054446	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487729	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491179	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12633707	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635736	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]
rs12639142	0.87[CHB][hapmap]
rs13070345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240859	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];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs339731	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34549959	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3846063	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3895740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3912104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3916334	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60706321	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6807878	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9830553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839430	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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
rs3907218	HHATL	cis	parietal	SCAN
rs3907218	HHATL	cis	cerebellum	SCAN
rs3907218	LRRC2	cis	cerebellum	SCAN
rs3907218	ZNF35	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
4	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:42774000-42777400	Weak transcription	Right Ventricle	heart
11	chr3:42774200-42777800	Weak transcription	Right Atrium	heart
12	chr3:42774200-42778200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:42774200-42778200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:42774600-42780800	Weak transcription	Psoas Muscle	Psoas
15	chr3:42774800-42776600	Enhancers	HepG2	liver
16	chr3:42774800-42777400	Weak transcription	Fetal Heart	heart
17	chr3:42774800-42778200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:42775000-42777400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:42775000-42777600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:42775200-42776800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:42775200-42777400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:42775200-42778000	Enhancers	Brain Angular Gyrus	brain
23	chr3:42775200-42778200	Enhancers	Brain Substantia Nigra	brain
24	chr3:42775400-42777400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:42775600-42777600	Enhancers	Brain Hippocampus Middle	brain
26	chr3:42775600-42778000	Enhancers	Brain Anterior Caudate	brain
27	chr3:42775600-42778200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:42775600-42778400	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:42775600-42781000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:42775800-42780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:42776000-42776800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:42776000-42777200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:42776400-42777200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:42776400-42777400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:42776400-42777800	Weak transcription	Spleen	Spleen
36	chr3:42776400-42778000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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