Variant report

Variant	rs9306890
Chromosome Location	chr2:20525948-20525949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20523318..20529381-chr2:20544822..20552572,11	K562	blood:
2	chr2:20525636..20526172-chr2:20578625..20579319,2	MCF-7	breast:
3	chr2:20525204..20529381-chr2:20546645..20551782,7	K562	blood:

Variant related genes	Relation type
ENSG00000055917	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10175853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187080	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1043400	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10460445	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460449	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460450	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495704	0.83[CEU][hapmap]
rs10856797	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11096648	0.92[CEU][hapmap]
rs11096654	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096655	0.80[JPT][hapmap]
rs11096659	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11690912	0.87[AFR][1000 genomes]
rs11888357	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895228	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896241	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11898408	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11900127	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902769	0.86[ASN][1000 genomes]
rs11903745	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12373772	0.96[CEU][hapmap]
rs12373819	0.96[CEU][hapmap]
rs12465832	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472685	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12473500	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474897	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12478265	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13393733	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17612703	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2072464	0.88[ASN][1000 genomes]
rs2080190	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2110410	0.80[CEU][hapmap]
rs2348703	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34678899	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732162	0.88[CEU][hapmap]
rs3771232	0.88[CEU][hapmap]
rs3771233	0.88[CEU][hapmap]
rs3771240	0.88[CEU][hapmap]
rs3771247	0.84[CEU][hapmap]
rs3796066	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3821218	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62123442	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748274	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72785217	0.88[ASN][1000 genomes]
rs72785218	0.88[ASN][1000 genomes]
rs72785278	0.88[ASN][1000 genomes]
rs72785282	0.87[ASN][1000 genomes]
rs72785297	0.88[ASN][1000 genomes]
rs72785298	0.88[ASN][1000 genomes]
rs72785300	0.88[ASN][1000 genomes]
rs72785301	0.88[ASN][1000 genomes]
rs72787406	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72787409	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72787411	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787415	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787433	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787499	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787501	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72788905	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558385	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs7579571	0.82[EUR][1000 genomes]
rs7582642	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585590	0.92[CEU][hapmap]
rs7595266	0.88[ASN][1000 genomes]
rs9306891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005366	chr2:20478859-20542134	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
3	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:20471800-20533800	Strong transcription	Dnd41	blood
5	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr2:20499200-20527600	Weak transcription	Small Intestine	intestine
8	chr2:20503000-20534600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:20505200-20526000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:20505200-20526600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:20507800-20527600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:20513800-20533000	Weak transcription	Right Ventricle	heart
13	chr2:20515200-20526800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:20515200-20527600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:20516800-20529600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:20516800-20536000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:20517800-20527000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:20517800-20527200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:20517800-20527600	Weak transcription	Pancreas	Pancrea
20	chr2:20517800-20530000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:20517800-20530000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:20517800-20533000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:20518000-20529200	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:20518000-20534400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:20518200-20526000	Weak transcription	Aorta	Aorta
26	chr2:20518200-20527400	Weak transcription	Esophagus	oesophagus
27	chr2:20518200-20530200	Weak transcription	Spleen	Spleen
28	chr2:20518400-20527200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:20518400-20527400	Weak transcription	HSMMtube	muscle
30	chr2:20518400-20530400	Weak transcription	Psoas Muscle	Psoas
31	chr2:20518600-20530200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:20519200-20530200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:20519600-20528200	Weak transcription	Fetal Brain Female	brain
34	chr2:20520800-20526600	Strong transcription	Hela-S3	cervix
35	chr2:20520800-20526600	Strong transcription	HSMM	muscle
36	chr2:20521200-20526400	Strong transcription	K562	blood
37	chr2:20521400-20526200	Strong transcription	Primary B cells from cord blood	blood
38	chr2:20521400-20534600	Weak transcription	Stomach Mucosa	stomach
39	chr2:20521800-20526200	Strong transcription	Fetal Intestine Large	intestine
40	chr2:20521800-20527200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:20522200-20526400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:20522200-20526800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:20522400-20526200	Strong transcription	NHEK	skin
44	chr2:20522400-20526600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:20522600-20526000	Strong transcription	NHDF-Ad	bronchial
46	chr2:20522600-20526600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:20522600-20527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:20522600-20530400	Weak transcription	Left Ventricle	heart
49	chr2:20522600-20530600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:20522600-20532400	Weak transcription	Colonic Mucosa	Colon

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