Variant report

Variant	rs16890474
Chromosome Location	chr6:25363683-25363684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434844	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1079960	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12525031	1.00[LWK][hapmap]
rs16890409	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs16890562	1.00[LWK][hapmap]
rs2223439	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4712910	0.81[ASN][1000 genomes]
rs4712911	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712928	1.00[LWK][hapmap]
rs926404	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9348673	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25359600-25366000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:25359800-25367200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25360000-25367200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:25360000-25367400	Weak transcription	Lung	lung
5	chr6:25360000-25367400	Weak transcription	Right Atrium	heart
6	chr6:25360400-25363800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:25360400-25366000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:25360400-25366400	Weak transcription	Gastric	stomach
9	chr6:25360400-25367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:25360400-25367600	Weak transcription	Pancreas	Pancrea
11	chr6:25360400-25367800	Weak transcription	Brain Germinal Matrix	brain
12	chr6:25360400-25369200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:25360600-25365600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:25360800-25367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:25360800-25367600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:25360800-25369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:25361000-25364200	Weak transcription	Fetal Thymus	thymus
18	chr6:25361000-25365000	Weak transcription	Ovary	ovary
19	chr6:25361000-25365600	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:25361000-25367000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:25361000-25367200	Weak transcription	Fetal Intestine Large	intestine
22	chr6:25361000-25367200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:25361000-25367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:25361000-25369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:25361000-25369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:25361000-25369400	Weak transcription	Left Ventricle	heart
27	chr6:25361000-25369800	Weak transcription	Brain Substantia Nigra	brain
28	chr6:25361200-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:25361200-25366600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:25361200-25367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:25361400-25365400	Weak transcription	Thymus	Thymus
32	chr6:25362000-25367000	Weak transcription	NHLF	lung
33	chr6:25362000-25367200	Weak transcription	Brain Anterior Caudate	brain
34	chr6:25362400-25363800	Enhancers	HMEC	breast
35	chr6:25362600-25364000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:25362600-25367200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:25362800-25366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:25362800-25367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:25363000-25364000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:25363000-25366000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:25363000-25366400	Weak transcription	NHEK	skin
42	chr6:25363200-25364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:25363200-25364400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:25363200-25364400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:25363200-25364600	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:25363200-25365400	Weak transcription	Aorta	Aorta
47	chr6:25363200-25365800	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr6:25363400-25363800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:25363400-25363800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:25363400-25363800	Enhancers	Fetal Lung	lung

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