Variant report

Variant	rs16841960
Chromosome Location	chr3:99887423-99887424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13326691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56233341	1.00[AMR][1000 genomes]
rs6762731	1.00[AMR][1000 genomes]
rs9867916	1.00[AMR][1000 genomes]
rs9876642	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:99868000-99897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:99869000-99895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:99869000-99897800	Weak transcription	Pancreas	Pancrea
6	chr3:99870400-99898600	Weak transcription	Esophagus	oesophagus
7	chr3:99871400-99899400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:99874400-99894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:99874400-99897000	Weak transcription	K562	blood
10	chr3:99874600-99897400	Weak transcription	A549	lung
11	chr3:99874800-99891000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:99874800-99895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:99874800-99897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:99874800-99897200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:99874800-99897200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:99874800-99898200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:99874800-99898400	Weak transcription	HepG2	liver
18	chr3:99875000-99897400	Weak transcription	GM12878-XiMat	blood
19	chr3:99875400-99890400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:99876400-99890400	Weak transcription	Primary B cells from cord blood	blood
21	chr3:99876400-99890800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:99876600-99889200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:99876600-99894800	Weak transcription	Right Atrium	heart
24	chr3:99876600-99897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:99876600-99897400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:99876800-99891600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:99877000-99888200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:99877600-99888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:99877600-99904600	Weak transcription	Right Ventricle	heart
30	chr3:99878000-99891000	Weak transcription	Fetal Brain Female	brain
31	chr3:99878000-99897200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:99878400-99897200	Weak transcription	Fetal Thymus	thymus
33	chr3:99878400-99898200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:99879000-99887800	Weak transcription	Fetal Lung	lung
35	chr3:99879200-99891000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:99879200-99894000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:99879200-99897400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:99879200-99897400	Weak transcription	NHEK	skin
39	chr3:99879200-99898600	Weak transcription	Hela-S3	cervix
40	chr3:99879400-99890800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:99879400-99896800	Weak transcription	Fetal Intestine Large	intestine
42	chr3:99879800-99888200	Weak transcription	Fetal Stomach	stomach
43	chr3:99879800-99891600	Weak transcription	NH-A	brain
44	chr3:99880000-99894400	Weak transcription	HSMM	muscle
45	chr3:99880200-99888600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:99880200-99889600	Weak transcription	Left Ventricle	heart
47	chr3:99880200-99897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:99880200-99898600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:99880400-99887800	Weak transcription	HUVEC	blood vessel
50	chr3:99880600-99894600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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