Variant report

Variant	rs123506
Chromosome Location	chr3:42775976-42775977
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	chr3:42727358..42730131-chr3:42775132..42777505,2	MCF-7	breast:
2	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs121993	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs123509	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339662	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs6865	1.00[CHB][hapmap]
rs735320	1.00[CHB][hapmap]
rs7641452	1.00[CHB][hapmap]
rs9865715	1.00[CHB][hapmap]

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

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:42769800-42787600	Weak transcription	Gastric	stomach
4	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
5	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:42773600-42776400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:42774000-42776400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:42774000-42776400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:42774000-42777400	Weak transcription	Right Ventricle	heart
15	chr3:42774200-42777800	Weak transcription	Right Atrium	heart
16	chr3:42774200-42778200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:42774200-42778200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:42774400-42776000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:42774400-42776000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:42774600-42780800	Weak transcription	Psoas Muscle	Psoas
21	chr3:42774800-42776600	Enhancers	HepG2	liver
22	chr3:42774800-42777400	Weak transcription	Fetal Heart	heart
23	chr3:42774800-42778200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:42775000-42777400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:42775000-42777600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:42775200-42776800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:42775200-42777400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:42775200-42778000	Enhancers	Brain Angular Gyrus	brain
29	chr3:42775200-42778200	Enhancers	Brain Substantia Nigra	brain
30	chr3:42775400-42777400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:42775600-42776400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:42775600-42777600	Enhancers	Brain Hippocampus Middle	brain
33	chr3:42775600-42778000	Enhancers	Brain Anterior Caudate	brain
34	chr3:42775600-42778200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:42775600-42778400	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:42775600-42781000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:42775800-42780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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