Variant report

Variant	rs16822378
Chromosome Location	chr3:191107023-191107024
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:190961402..190962676-chr3:191106356..191107443,7	MCF-7	breast:
2	chr3:190853421..190854274-chr3:191106763..191107318,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11542549	0.90[ASN][1000 genomes]
rs1435062	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473869	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1520202	0.87[EUR][1000 genomes]
rs1520203	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs1609926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16822382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848980	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs16866487	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16866504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16866505	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17753967	0.95[ASN][1000 genomes]
rs17810246	0.95[ASN][1000 genomes]
rs17810282	0.95[ASN][1000 genomes]
rs17838893	0.82[ASN][1000 genomes]
rs2056333	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2364379	0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28715898	0.95[ASN][1000 genomes]
rs366757	0.81[AFR][1000 genomes]
rs3796219	0.87[EUR][1000 genomes]
rs3959143	0.99[ASN][1000 genomes]
rs4677631	0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4677632	0.95[ASN][1000 genomes]
rs4677725	0.95[ASN][1000 genomes]
rs4677726	0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4677727	0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs56174842	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57211729	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58141749	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58645265	0.90[ASN][1000 genomes]
rs59709586	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61250936	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6444541	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs73185209	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73185210	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73185213	0.90[ASN][1000 genomes]
rs73185226	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73185228	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73185240	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73185255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73185263	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185284	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73185287	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73185288	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73201627	0.87[EUR][1000 genomes]
rs73201628	0.93[EUR][1000 genomes]
rs73201630	0.93[EUR][1000 genomes]
rs73201631	0.93[EUR][1000 genomes]
rs7637196	0.90[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs7642387	0.95[ASN][1000 genomes]
rs7648886	0.95[ASN][1000 genomes]
rs9290986	0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs9823680	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs9824437	0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs9839751	0.81[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs9843934	0.95[ASN][1000 genomes]
rs9853569	0.95[ASN][1000 genomes]
rs9863255	0.93[ASN][1000 genomes]
rs9876944	0.96[ASN][1000 genomes]

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	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:191079600-191121200	Weak transcription	Gastric	stomach
5	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
7	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
14	chr3:191094800-191114800	Weak transcription	A549	lung
15	chr3:191095000-191107600	Weak transcription	Fetal Intestine Small	intestine
16	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:191096400-191109600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:191096600-191114800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:191097200-191109200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:191098000-191111400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
22	chr3:191099600-191113800	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:191099600-191114000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:191099600-191114600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:191099800-191117600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:191100200-191107200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:191100200-191108200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:191100200-191108400	Weak transcription	Ovary	ovary
30	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
31	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
32	chr3:191100200-191119600	Weak transcription	K562	blood
33	chr3:191100400-191107200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:191100400-191108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:191100400-191114000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:191100400-191117400	Weak transcription	Fetal Stomach	stomach
37	chr3:191100400-191117400	Weak transcription	Lung	lung
38	chr3:191100400-191117800	Weak transcription	Small Intestine	intestine
39	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
40	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
41	chr3:191100600-191107200	Weak transcription	Aorta	Aorta
42	chr3:191100600-191107400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:191100600-191109400	Weak transcription	Primary T cells from cord blood	blood
44	chr3:191100800-191115400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:191101000-191107400	Weak transcription	Placenta	Placenta
46	chr3:191101000-191108400	Weak transcription	NHLF	lung
47	chr3:191101000-191108800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:191101000-191115600	Weak transcription	Fetal Kidney	kidney
49	chr3:191101000-191117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:191101200-191107200	Weak transcription	Primary monocytes fromperipheralblood	blood

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