Variant report

Variant	rs2005557
Chromosome Location	chr3:49701298-49701299
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	chr3:49575972..49578026-chr3:49699559..49702173,2	K562	blood:
2	chr3:49696156..49697699-chr3:49699685..49702329,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1060962	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130212	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130213	0.85[ASN][1000 genomes]
rs11709525	0.81[ASN][1000 genomes]
rs11710037	0.81[ASN][1000 genomes]
rs11718165	0.91[ASN][1000 genomes]
rs11919311	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12490267	0.87[EUR][1000 genomes]
rs12497288	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13316695	0.81[ASN][1000 genomes]
rs1352890	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1826347	1.00[CEU][hapmap]
rs1873626	1.00[CEU][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131104	1.00[CEU][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]
rs2131109	1.00[CEU][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172252	0.81[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960548	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34762726	0.81[ASN][1000 genomes]
rs35007338	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35404120	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283605	0.81[ASN][1000 genomes]
rs4855835	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4855847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855852	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855881	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855883	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855884	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765869	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767878	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6770670	0.81[ASN][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs9812791	0.81[ASN][1000 genomes]
rs9823546	0.91[ASN][1000 genomes]
rs9824092	0.81[ASN][1000 genomes]
rs9836291	0.91[ASN][1000 genomes]
rs9858542	0.91[ASN][1000 genomes]
rs9862080	0.81[ASN][1000 genomes]
rs9882740	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49702400	Weak transcription	Right Ventricle	heart
5	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:49690400-49702000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49693200-49703200	Weak transcription	Gastric	stomach
10	chr3:49695000-49702000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:49695800-49704000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:49696600-49701400	Weak transcription	HepG2	liver
14	chr3:49696600-49701800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:49698400-49702200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:49699600-49702800	Weak transcription	Pancreas	Pancrea
17	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
18	chr3:49700200-49701400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49700200-49701800	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49700400-49701600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49700400-49701800	Strong transcription	Brain Angular Gyrus	brain
22	chr3:49700800-49701400	Strong transcription	Brain Cingulate Gyrus	brain
23	chr3:49700800-49704400	Strong transcription	Brain Anterior Caudate	brain
24	chr3:49701000-49702000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49701200-49702200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
26	chr3:49701200-49703400	Enhancers	Liver	Liver

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