Variant report

Variant	rs16823149
Chromosome Location	chr1:184402508-184402509
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	chr1:184393745..184397923-chr1:184400425..184402634,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10157833	0.90[ASN][1000 genomes]
rs10158710	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs10489721	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489722	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752935	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10797966	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10911593	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10911594	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10911595	0.84[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11802306	0.93[ASN][1000 genomes]
rs11805001	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11810399	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs11811039	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12048492	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12057850	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12058294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12063210	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12063636	0.85[EUR][1000 genomes]
rs12070409	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12070712	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12079094	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12085285	0.91[EUR][1000 genomes]
rs12088034	0.89[EUR][1000 genomes]
rs12093839	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1535135	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs16823097	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16823101	1.00[CEU][hapmap]
rs1884201	0.89[EUR][1000 genomes]
rs1884202	0.88[EUR][1000 genomes]
rs1884203	0.88[EUR][1000 genomes]
rs1969686	0.82[ASN][1000 genomes]
rs2207522	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2207523	0.86[EUR][1000 genomes]
rs3916684	0.85[EUR][1000 genomes]
rs3930803	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233119	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4326589	1.00[CEU][hapmap]
rs4518858	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs57024489	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57073878	0.91[EUR][1000 genomes]
rs57790643	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58462114	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59369289	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61502552	0.89[EUR][1000 genomes]
rs61823501	0.82[ASN][1000 genomes]
rs61823506	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61823538	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61823539	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61823542	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823543	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61823546	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424948	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6424949	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6424950	1.00[CEU][hapmap]
rs6656089	0.93[ASN][1000 genomes]
rs6657105	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657254	0.86[ASN][1000 genomes]
rs6660217	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6666696	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs6688074	0.88[EUR][1000 genomes]
rs6696161	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6696270	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs72735678	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732959	0.91[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7415961	1.00[CEU][hapmap]
rs7512266	0.86[EUR][1000 genomes]
rs7522628	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7537725	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538587	0.94[EUR][1000 genomes]
rs7540361	0.84[EUR][1000 genomes];0.89[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184383800-184412400	Weak transcription	Fetal Stomach	stomach
2	chr1:184387200-184403400	Weak transcription	Aorta	Aorta
3	chr1:184390600-184422400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:184392200-184408200	Weak transcription	Esophagus	oesophagus
5	chr1:184395000-184405600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:184395200-184405000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:184395400-184408000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:184395800-184405600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:184396000-184412800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:184396200-184412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:184396200-184418800	Weak transcription	NHEK	skin
12	chr1:184396200-184419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:184396400-184430000	Weak transcription	Spleen	Spleen
14	chr1:184396800-184404800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:184398200-184402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:184398200-184404600	Weak transcription	Lung	lung
17	chr1:184398400-184403400	Weak transcription	Left Ventricle	heart
18	chr1:184398400-184403400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:184398400-184405000	Weak transcription	Right Ventricle	heart
20	chr1:184398400-184405200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:184398400-184410200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:184398600-184411400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:184398800-184403400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:184398800-184418800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:184400400-184412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:184402200-184402600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr1:184402200-184402600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:184402200-184402600	Enhancers	Psoas Muscle	Psoas
29	chr1:184402200-184403000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:184402200-184403400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:184402200-184405600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:184402400-184402600	Enhancers	Fetal Lung	lung
33	chr1:184402400-184403000	Weak transcription	Right Atrium	heart
34	chr1:184402400-184403600	Enhancers	Stomach Mucosa	stomach
35	chr1:184402400-184406600	Weak transcription	Pancreas	Pancrea

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