Variant report

Variant	rs16847488
Chromosome Location	chr1:227421870-227421871
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	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242757	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10458373	0.84[ASN][1000 genomes]
rs10458378	0.84[ASN][1000 genomes]
rs10495261	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10495262	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10495264	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10799385	0.85[ASN][1000 genomes]
rs10799386	0.85[ASN][1000 genomes]
rs10799389	0.84[ASN][1000 genomes]
rs10799392	0.86[ASN][1000 genomes]
rs10799393	0.86[ASN][1000 genomes]
rs10799394	0.86[ASN][1000 genomes]
rs10799395	0.86[ASN][1000 genomes]
rs10916091	0.85[ASN][1000 genomes]
rs10916093	0.84[ASN][1000 genomes]
rs10916094	0.85[ASN][1000 genomes]
rs10916096	0.86[ASN][1000 genomes]
rs10916099	0.82[CHB][hapmap]
rs11800145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800705	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11804358	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11808884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11808903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810506	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12063170	0.85[ASN][1000 genomes]
rs12139502	0.84[ASN][1000 genomes]
rs12142938	0.85[ASN][1000 genomes]
rs12410431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1513623	0.86[ASN][1000 genomes]
rs16846854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16846892	1.00[AFR][1000 genomes]
rs16846989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1877620	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1929853	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2090008	0.84[ASN][1000 genomes]
rs2203280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2225508	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2492629	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2670442	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2718221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813962	0.81[CHB][hapmap]
rs2813971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122331	0.82[ASN][1000 genomes]
rs4653481	0.85[ASN][1000 genomes]
rs4653816	0.83[CHB][hapmap]
rs4653817	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs4653827	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs477162	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs484150	0.82[ASN][1000 genomes]
rs489565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs490517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs497291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs511679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs512538	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs529430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs537004	0.82[ASN][1000 genomes]
rs545171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs555786	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs558921	0.82[ASN][1000 genomes]
rs572561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs583729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs602585	0.83[ASN][1000 genomes]
rs629571	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6426567	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6426568	0.85[ASN][1000 genomes]
rs6426569	0.86[ASN][1000 genomes]
rs664617	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs664815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6656723	0.85[ASN][1000 genomes]
rs6661802	0.82[ASN][1000 genomes]
rs6664251	0.85[ASN][1000 genomes]
rs6672658	0.84[ASN][1000 genomes]
rs6675179	0.82[ASN][1000 genomes]
rs6675599	0.86[ASN][1000 genomes]
rs6681424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6685830	0.86[ASN][1000 genomes]
rs6690771	0.84[ASN][1000 genomes]
rs6695787	0.84[ASN][1000 genomes]
rs6700137	0.84[ASN][1000 genomes]
rs6700338	0.84[ASN][1000 genomes]
rs6702869	0.85[ASN][1000 genomes]
rs7365134	0.84[ASN][1000 genomes]
rs7367807	0.84[ASN][1000 genomes]
rs7517177	0.85[ASN][1000 genomes]
rs7517646	0.84[ASN][1000 genomes]
rs7524042	0.84[ASN][1000 genomes]
rs7524731	0.84[ASN][1000 genomes]
rs7531576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7538743	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7539423	0.82[CHB][hapmap]
rs9426540	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs9426545	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9426606	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227414200-227423400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:227414200-227453800	Weak transcription	HSMM	muscle
16	chr1:227414400-227422200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:227414400-227422400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:227414400-227422400	Weak transcription	K562	blood
19	chr1:227414400-227423000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:227414400-227423000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:227415400-227422200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:227415600-227422800	Weak transcription	HUVEC	blood vessel
27	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
30	chr1:227421800-227422000	Enhancers	Gastric	stomach
31	chr1:227421800-227422000	Enhancers	Ovary	ovary
32	chr1:227421800-227422000	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:227421800-227423000	Enhancers	Left Ventricle	heart

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