Variant report

Variant	rs16864396
Chromosome Location	chr1:171296762-171296763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16864312	1.00[JPT][hapmap]
rs16864314	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864332	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864359	1.00[AMR][1000 genomes]
rs16864362	1.00[AMR][1000 genomes]
rs16864364	1.00[AMR][1000 genomes]
rs16864389	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16864392	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16864395	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16864417	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2038097	1.00[AMR][1000 genomes]
rs28360434	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs45443493	1.00[AMR][1000 genomes]
rs45452395	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45458993	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45490301	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45508097	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45520235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45552133	1.00[AMR][1000 genomes]
rs45560645	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45569734	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45571236	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45579736	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45627437	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6674736	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6685422	1.00[JPT][hapmap]
rs6699241	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs717023	0.87[ASW][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs717024	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7543159	1.00[JPT][hapmap]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr1:171283600-171297800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:171284000-171312200	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:171284200-171307400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:171284200-171313600	Weak transcription	Right Ventricle	heart
5	chr1:171284200-171313800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:171286800-171309200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:171288400-171313000	Weak transcription	Gastric	stomach
8	chr1:171288600-171299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:171288600-171303000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:171288600-171303800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:171288600-171312400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:171289400-171299400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:171289400-171301000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:171289400-171309600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:171289400-171313400	Weak transcription	Fetal Lung	lung
16	chr1:171289600-171309000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:171289600-171309000	Weak transcription	Pancreas	Pancrea
18	chr1:171289600-171313000	Weak transcription	Adipose Nuclei	Adipose
19	chr1:171289800-171298000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:171289800-171298000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:171289800-171298200	Weak transcription	Aorta	Aorta
22	chr1:171289800-171299600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:171289800-171300200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:171289800-171300600	Weak transcription	Primary T cells from cord blood	blood
25	chr1:171289800-171309000	Weak transcription	Spleen	Spleen
26	chr1:171289800-171309200	Weak transcription	Left Ventricle	heart
27	chr1:171289800-171312600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:171289800-171313000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:171290000-171308200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:171290000-171309200	Weak transcription	Ovary	ovary
31	chr1:171292200-171297000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:171294400-171297000	Enhancers	Fetal Heart	heart
33	chr1:171296200-171299000	Enhancers	Liver	Liver
34	chr1:171296600-171298000	Weak transcription	Fetal Intestine Large	intestine
35	chr1:171296600-171298000	Weak transcription	Fetal Intestine Small	intestine

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