Variant report

Variant	rs16973231
Chromosome Location	chr19:39635946-39635947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39630404..39632300-chr19:39634611..39637101,2	MCF-7	breast:
2	chr19:39635749..39637767-chr19:39638007..39640559,2	K562	blood:
3	chr19:39521227..39522837-chr19:39634910..39636510,2	K562	blood:
4	chr19:39633693..39637840-chr19:39657942..39661020,3	MCF-7	breast:
5	chr19:39635690..39638303-chr19:39642762..39645272,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11878229	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11878648	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879084	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879196	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879341	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880984	1.00[EUR][1000 genomes]
rs11881029	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882668	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882711	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882955	1.00[EUR][1000 genomes]
rs16973211	0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57716250	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57769351	1.00[EUR][1000 genomes]
rs58626126	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58909586	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59303188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60229944	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61641657	1.00[EUR][1000 genomes]
rs7246294	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254424	1.00[EUR][1000 genomes]
rs7260015	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549583	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549585	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549593	1.00[AMR][1000 genomes]
rs73549600	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551720	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551743	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551744	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551752	0.90[AFR][1000 genomes]
rs73551786	1.00[EUR][1000 genomes]
rs73553708	1.00[EUR][1000 genomes]
rs73553711	1.00[EUR][1000 genomes]
rs73553738	1.00[EUR][1000 genomes]
rs73553740	1.00[EUR][1000 genomes]
rs73553742	1.00[EUR][1000 genomes]
rs73930290	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73930300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73933809	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73933837	1.00[EUR][1000 genomes]
rs8101586	1.00[EUR][1000 genomes]
rs8111473	0.83[YRI][hapmap];1.00[EUR][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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
3	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:39622600-39639600	Weak transcription	HSMM	muscle
5	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39624000-39647000	Weak transcription	NHLF	lung
7	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:39627600-39641200	Weak transcription	Hela-S3	cervix
9	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:39629200-39639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:39629600-39637600	Genic enhancers	Fetal Intestine Small	intestine
12	chr19:39630800-39646800	Weak transcription	Osteobl	bone
13	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
14	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:39631200-39637200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:39631800-39639400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:39631800-39640800	Weak transcription	K562	blood
18	chr19:39631800-39644600	Weak transcription	Primary T cells from cord blood	blood
19	chr19:39632600-39637400	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:39633000-39637400	Enhancers	Placenta	Placenta
21	chr19:39633800-39636200	Weak transcription	Gastric	stomach
22	chr19:39634400-39637400	Enhancers	Duodenum Mucosa	Duodenum
23	chr19:39634600-39636800	Enhancers	HUVEC	blood vessel
24	chr19:39634600-39637000	Enhancers	Fetal Lung	lung
25	chr19:39634600-39637000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr19:39634600-39637400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:39634600-39638200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr19:39634800-39636000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:39634800-39636000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr19:39634800-39636000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:39634800-39636000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:39634800-39636200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr19:39634800-39636400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr19:39634800-39636400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:39634800-39636400	Enhancers	Adipose Nuclei	Adipose
36	chr19:39634800-39636800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:39634800-39636800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39634800-39636800	Enhancers	Fetal Brain Male	brain
39	chr19:39634800-39636800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr19:39634800-39636800	Enhancers	HMEC	breast
41	chr19:39634800-39637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:39634800-39637000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr19:39634800-39637000	Enhancers	Right Atrium	heart
44	chr19:39634800-39637000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr19:39634800-39637200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr19:39634800-39637200	Enhancers	Fetal Muscle Leg	muscle
47	chr19:39634800-39637400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:39634800-39637400	Enhancers	Lung	lung
49	chr19:39634800-39637400	Enhancers	Pancreas	Pancrea
50	chr19:39634800-39637400	Enhancers	Stomach Mucosa	stomach

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