Variant report

Variant	rs10816490
Chromosome Location	chr9:110073580-110073581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110068615..110071443-chr9:110072846..110075913,3	MCF-7	breast:
2	chr9:110044300..110048942-chr9:110067094..110074281,11	MCF-7	breast:
3	chr9:110044399..110049612-chr9:110071012..110080286,12	K562	blood:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10113916	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119641	0.88[ASN][1000 genomes]
rs10122970	0.87[ASN][1000 genomes]
rs10481632	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10521083	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10739234	0.92[AFR][1000 genomes]
rs10739236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739238	0.92[AFR][1000 genomes]
rs10816477	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816480	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816485	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816491	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978775	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978776	0.87[ASN][1000 genomes]
rs10978777	0.87[ASN][1000 genomes]
rs10978791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342066	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12345455	0.87[ASN][1000 genomes]
rs12555417	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1535765	0.85[AFR][1000 genomes]
rs1805329	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805334	0.80[EUR][1000 genomes]
rs1886134	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1969798	0.80[AFR][1000 genomes]
rs1980725	0.80[AFR][1000 genomes]
rs2005143	0.82[ASN][1000 genomes]
rs2147071	0.85[AFR][1000 genomes]
rs2417776	0.87[ASN][1000 genomes]
rs2417784	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28534368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28769087	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28848858	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4278207	0.83[EUR][1000 genomes]
rs4625087	0.84[AFR][1000 genomes]
rs4978404	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4978406	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4978849	0.92[AFR][1000 genomes]
rs61701375	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs698475	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025563	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7029997	0.85[AFR][1000 genomes]
rs7030169	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7030555	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7030631	0.85[AFR][1000 genomes]
rs7031906	0.80[AFR][1000 genomes]
rs7035611	0.92[AFR][1000 genomes]
rs7036284	0.87[ASN][1000 genomes]
rs7038737	0.92[AFR][1000 genomes]
rs7039041	0.92[AFR][1000 genomes]
rs7040217	0.96[ASN][1000 genomes]
rs7041137	0.96[ASN][1000 genomes]
rs7041497	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7043962	0.86[AFR][1000 genomes]
rs7046950	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7856227	0.92[AFR][1000 genomes]
rs7873745	0.86[ASN][1000 genomes]
rs817836	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817838	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817839	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817840	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817841	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817843	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817844	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817845	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817846	0.88[AFR][1000 genomes]
rs817847	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817849	0.88[ASN][1000 genomes]
rs817851	0.88[ASN][1000 genomes]
rs942291	0.87[ASN][1000 genomes]
rs942293	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9632893	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969728	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:110057200-110079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:110057400-110074600	Weak transcription	Spleen	Spleen
4	chr9:110057400-110074800	Weak transcription	Psoas Muscle	Psoas
5	chr9:110058600-110074800	Weak transcription	Right Atrium	heart
6	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
7	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:110062000-110076000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:110062000-110078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:110062400-110077800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:110062400-110078600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:110062600-110078800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:110062800-110077600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:110063000-110077200	Strong transcription	A549	lung
15	chr9:110063000-110078200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr9:110063000-110079200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:110063200-110077400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:110063200-110077400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr9:110063200-110077800	Strong transcription	Placenta	Placenta
20	chr9:110063400-110077800	Strong transcription	Fetal Lung	lung
21	chr9:110063600-110078600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:110063800-110079200	Strong transcription	Osteobl	bone
23	chr9:110063800-110079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:110064000-110074400	Strong transcription	HSMM	muscle
25	chr9:110064000-110074600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:110064000-110074600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:110064000-110085000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:110065200-110089200	Strong transcription	Fetal Thymus	thymus
29	chr9:110065400-110077800	Strong transcription	Primary B cells from cord blood	blood
30	chr9:110065600-110098600	Strong transcription	Dnd41	blood
31	chr9:110067000-110077800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr9:110067400-110076600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:110068400-110077200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr9:110068600-110074400	Strong transcription	Adipose Nuclei	Adipose
35	chr9:110068600-110077400	Strong transcription	HUVEC	blood vessel
36	chr9:110069000-110074400	Weak transcription	Pancreas	Pancrea
37	chr9:110069000-110074600	Weak transcription	Gastric	stomach
38	chr9:110069000-110074800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:110069800-110074600	Weak transcription	Aorta	Aorta
40	chr9:110069800-110074600	Weak transcription	Fetal Stomach	stomach
41	chr9:110070000-110074200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:110070000-110074200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:110070000-110074600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:110070200-110074200	Strong transcription	NHDF-Ad	bronchial
45	chr9:110070200-110074400	Weak transcription	Brain Germinal Matrix	brain
46	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr9:110070400-110074400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:110070400-110074400	Weak transcription	NHEK	skin
49	chr9:110070400-110085000	Weak transcription	Colonic Mucosa	Colon
50	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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