Variant report

Variant	rs59938221
Chromosome Location	chr10:98617641-98617642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98590420..98592007-chr10:98615843..98619097,3	K562	blood:
2	chr10:98615796..98618493-chr10:98618946..98621745,3	MCF-7	breast:
3	chr10:98607034..98609759-chr10:98615492..98617827,2	MCF-7	breast:
4	chr10:98601468..98603302-chr10:98616788..98619588,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10437452	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11188937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188939	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188940	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188954	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188955	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188956	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188959	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188967	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188971	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11188978	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12241405	0.88[EUR][1000 genomes]
rs12241564	0.84[EUR][1000 genomes]
rs12242330	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243551	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244490	0.93[EUR][1000 genomes]
rs12246067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247344	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249427	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249891	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252424	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257413	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258355	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258469	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261881	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263331	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264014	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12265242	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266185	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267926	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268216	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268272	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376965	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112175	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112190	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183449	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28439735	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28758432	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56867696	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408003	0.86[ASN][1000 genomes]
rs57501540	0.88[EUR][1000 genomes]
rs57716318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58376960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59751908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59999388	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576681	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61492214	0.96[EUR][1000 genomes]
rs6584101	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7071211	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7072273	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073150	0.82[EUR][1000 genomes]
rs7082316	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7085822	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085851	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086875	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7090441	0.87[EUR][1000 genomes]
rs7090690	0.86[EUR][1000 genomes]
rs74153734	0.93[EUR][1000 genomes]
rs7893144	0.83[ASN][1000 genomes]
rs7893325	0.82[EUR][1000 genomes]
rs7893564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.89[EUR][1000 genomes]
rs7894418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7906294	0.89[EUR][1000 genomes]
rs7910221	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920238	0.86[EUR][1000 genomes]
rs7921193	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921216	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv825532	chr10:98567434-98618034	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98593800-98624200	Weak transcription	Colonic Mucosa	Colon
2	chr10:98594200-98639400	Weak transcription	Thymus	Thymus
3	chr10:98594400-98618800	Weak transcription	Fetal Stomach	stomach
4	chr10:98597600-98618000	Weak transcription	Dnd41	blood
5	chr10:98600200-98624000	Weak transcription	Fetal Brain Male	brain
6	chr10:98602200-98621200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:98603000-98618200	Weak transcription	Fetal Kidney	kidney
8	chr10:98603200-98618200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr10:98603200-98619600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr10:98603200-98620000	Weak transcription	Hela-S3	cervix
11	chr10:98603200-98621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:98604600-98623400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:98604800-98617800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr10:98604800-98623600	Weak transcription	Fetal Brain Female	brain
15	chr10:98605200-98618200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:98605200-98619600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr10:98606200-98623200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:98606800-98623600	Weak transcription	Stomach Mucosa	stomach
19	chr10:98607000-98624000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr10:98610600-98618000	Weak transcription	Small Intestine	intestine
21	chr10:98610600-98622000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:98610800-98619400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:98610800-98632200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:98611000-98618200	Weak transcription	Fetal Lung	lung
25	chr10:98611000-98618400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:98611000-98620000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr10:98611000-98621600	Weak transcription	Placenta	Placenta
28	chr10:98611000-98623200	Weak transcription	A549	lung
29	chr10:98611000-98649800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:98611000-98713000	Weak transcription	Aorta	Aorta
31	chr10:98611200-98618600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:98611200-98623400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr10:98611200-98623600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr10:98611200-98623600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr10:98611200-98640200	Weak transcription	Fetal Heart	heart
36	chr10:98611400-98620000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:98611600-98619600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:98612200-98623400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:98613200-98618200	Weak transcription	Right Ventricle	heart
40	chr10:98613800-98618600	Weak transcription	Fetal Thymus	thymus
41	chr10:98613800-98619600	Weak transcription	Esophagus	oesophagus
42	chr10:98614000-98623400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:98615600-98618200	Enhancers	Primary B cells from peripheral blood	blood
44	chr10:98616000-98617800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:98616000-98618400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:98616000-98618400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr10:98616200-98617800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr10:98616200-98617800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:98616200-98618200	Enhancers	Brain Germinal Matrix	brain
50	chr10:98616200-98618400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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