Variant report

Variant	rs28377416
Chromosome Location	chr3:179833944-179833945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10513775	1.00[EUR][1000 genomes]
rs11916351	1.00[EUR][1000 genomes]
rs11919129	1.00[EUR][1000 genomes]
rs11922852	1.00[EUR][1000 genomes]
rs11923122	1.00[EUR][1000 genomes]
rs11924444	1.00[EUR][1000 genomes]
rs11929056	1.00[EUR][1000 genomes]
rs13320900	1.00[EUR][1000 genomes]
rs13324315	1.00[EUR][1000 genomes]
rs13327114	1.00[EUR][1000 genomes]
rs13327183	1.00[EUR][1000 genomes]
rs1543266	1.00[EUR][1000 genomes]
rs16831253	1.00[EUR][1000 genomes]
rs16831270	1.00[EUR][1000 genomes]
rs2090762	1.00[EUR][1000 genomes]
rs28373443	1.00[EUR][1000 genomes]
rs28545820	1.00[EUR][1000 genomes]
rs28623139	1.00[EUR][1000 genomes]
rs28701054	1.00[EUR][1000 genomes]
rs28726303	1.00[EUR][1000 genomes]
rs28736488	1.00[EUR][1000 genomes]
rs28758960	1.00[EUR][1000 genomes]
rs2879655	1.00[EUR][1000 genomes]
rs4499599	1.00[EUR][1000 genomes]
rs4621328	1.00[EUR][1000 genomes]
rs56406807	1.00[EUR][1000 genomes]
rs57727445	1.00[EUR][1000 genomes]
rs60008753	1.00[EUR][1000 genomes]
rs6765080	1.00[EUR][1000 genomes]
rs6765906	1.00[EUR][1000 genomes]
rs6776289	1.00[EUR][1000 genomes]
rs6777029	1.00[EUR][1000 genomes]
rs6779403	1.00[EUR][1000 genomes]
rs6787700	1.00[EUR][1000 genomes]
rs6795109	1.00[EUR][1000 genomes]
rs6797862	1.00[EUR][1000 genomes]
rs6804532	1.00[EUR][1000 genomes]
rs6809894	1.00[EUR][1000 genomes]
rs73055498	1.00[EUR][1000 genomes]
rs73883804	1.00[EUR][1000 genomes]
rs73885453	1.00[EUR][1000 genomes]
rs73885465	1.00[EUR][1000 genomes]
rs73885473	1.00[EUR][1000 genomes]
rs73885496	1.00[EUR][1000 genomes]
rs7612350	1.00[EUR][1000 genomes]
rs7614651	1.00[EUR][1000 genomes]
rs7628443	1.00[EUR][1000 genomes]
rs7635460	1.00[EUR][1000 genomes]
rs7646970	1.00[EUR][1000 genomes]
rs9290693	1.00[EUR][1000 genomes]
rs9290694	1.00[EUR][1000 genomes]
rs9290698	1.00[EUR][1000 genomes]
rs9815044	1.00[EUR][1000 genomes]
rs9818567	1.00[EUR][1000 genomes]
rs9819315	1.00[EUR][1000 genomes]
rs9825264	1.00[EUR][1000 genomes]
rs9825542	1.00[EUR][1000 genomes]
rs9826576	1.00[EUR][1000 genomes]
rs9827331	1.00[EUR][1000 genomes]
rs9828833	1.00[EUR][1000 genomes]
rs9830454	1.00[EUR][1000 genomes]
rs9830623	1.00[EUR][1000 genomes]
rs9832076	1.00[EUR][1000 genomes]
rs9836941	1.00[EUR][1000 genomes]
rs9841268	1.00[EUR][1000 genomes]
rs9841642	1.00[EUR][1000 genomes]
rs9841905	1.00[EUR][1000 genomes]
rs9842405	1.00[EUR][1000 genomes]
rs9844266	1.00[EUR][1000 genomes]
rs9844627	1.00[EUR][1000 genomes]
rs9844929	1.00[EUR][1000 genomes]
rs9845131	1.00[EUR][1000 genomes]
rs9846836	1.00[EUR][1000 genomes]
rs9849568	1.00[EUR][1000 genomes]
rs9852228	1.00[EUR][1000 genomes]
rs9856995	1.00[EUR][1000 genomes]
rs9858982	1.00[EUR][1000 genomes]
rs9859460	1.00[EUR][1000 genomes]
rs9861136	1.00[EUR][1000 genomes]
rs9862085	1.00[EUR][1000 genomes]
rs9863397	1.00[EUR][1000 genomes]
rs9863949	1.00[EUR][1000 genomes]
rs9871675	1.00[EUR][1000 genomes]
rs9872191	1.00[EUR][1000 genomes]
rs9872323	1.00[EUR][1000 genomes]
rs9872365	1.00[EUR][1000 genomes]
rs9873559	1.00[EUR][1000 genomes]
rs9877145	1.00[EUR][1000 genomes]
rs9884094	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012880	chr3:179772283-179835563	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179810600-179843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179828200-179835000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:179831800-179835400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:179832000-179834200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:179832000-179835200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:179832200-179834200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:179832200-179835400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:179832200-179836400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:179832200-179836400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:179832400-179834400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:179832400-179835800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:179832600-179834400	Weak transcription	Ovary	ovary
13	chr3:179832600-179835600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:179832800-179836000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:179833000-179834000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:179833400-179834400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:179833800-179834000	Enhancers	Brain Substantia Nigra	brain

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