Variant report

Variant	rs12249891
Chromosome Location	chr10:98604917-98604918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98589501..98594429-chr10:98600475..98606704,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196233	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10437452	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11188929	0.80[EUR][1000 genomes]
rs11188937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188939	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188940	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188954	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188955	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188956	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188959	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188967	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188971	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11188978	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12241405	0.84[EUR][1000 genomes]
rs12241564	0.81[EUR][1000 genomes]
rs12242330	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243551	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244490	0.96[EUR][1000 genomes]
rs12246067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247344	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249427	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252424	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257413	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258355	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258469	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261881	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263331	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264014	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12265242	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266185	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267926	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268216	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268272	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376965	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112175	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112190	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183449	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28439735	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28758432	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56867696	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408003	0.86[ASN][1000 genomes]
rs57501540	0.84[EUR][1000 genomes]
rs57716318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58376960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59751908	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59938221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59999388	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576681	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61492214	0.93[EUR][1000 genomes]
rs6584101	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7071211	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7072273	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	0.88[EUR][1000 genomes]
rs7085822	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085851	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086875	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7090441	0.84[EUR][1000 genomes]
rs7090690	0.82[EUR][1000 genomes]
rs7090880	0.80[EUR][1000 genomes]
rs73318641	0.80[EUR][1000 genomes]
rs74153734	0.96[EUR][1000 genomes]
rs7893144	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7893564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.86[EUR][1000 genomes]
rs7894418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7906294	0.86[EUR][1000 genomes]
rs7910221	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920238	0.82[EUR][1000 genomes]
rs7921193	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921216	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	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	nsv1053801	chr10:98506832-98610101	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98593800-98606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:98593800-98624200	Weak transcription	Colonic Mucosa	Colon
3	chr10:98594200-98610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:98594200-98610800	Weak transcription	Fetal Thymus	thymus
5	chr10:98594200-98639400	Weak transcription	Thymus	Thymus
6	chr10:98594400-98618800	Weak transcription	Fetal Stomach	stomach
7	chr10:98595800-98610400	Weak transcription	Aorta	Aorta
8	chr10:98596000-98610400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:98596200-98610400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:98596200-98616200	Weak transcription	Brain Germinal Matrix	brain
11	chr10:98596400-98613000	Weak transcription	Fetal Muscle Leg	muscle
12	chr10:98596400-98616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:98596600-98607400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr10:98596600-98616000	Weak transcription	Gastric	stomach
15	chr10:98597600-98605000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:98597600-98610400	Weak transcription	Fetal Heart	heart
17	chr10:98597600-98618000	Weak transcription	Dnd41	blood
18	chr10:98600200-98624000	Weak transcription	Fetal Brain Male	brain
19	chr10:98600400-98605400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr10:98601000-98607400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:98601000-98609800	Weak transcription	NHDF-Ad	bronchial
22	chr10:98601000-98610000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:98601000-98610400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:98601000-98610600	Weak transcription	GM12878-XiMat	blood
25	chr10:98601000-98612800	Weak transcription	Psoas Muscle	Psoas
26	chr10:98601200-98610000	Weak transcription	NH-A	brain
27	chr10:98601200-98610200	Weak transcription	HSMM	muscle
28	chr10:98601400-98610400	Weak transcription	Primary B cells from cord blood	blood
29	chr10:98602200-98605000	Enhancers	Primary T cells from cord blood	blood
30	chr10:98602200-98621200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:98602400-98606800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr10:98602600-98610200	Weak transcription	Small Intestine	intestine
33	chr10:98602800-98605000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr10:98602800-98606400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:98603000-98605200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:98603000-98610600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:98603000-98617200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:98603000-98618200	Weak transcription	Fetal Kidney	kidney
39	chr10:98603200-98605600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:98603200-98605600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr10:98603200-98605800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr10:98603200-98605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:98603200-98605800	Weak transcription	Esophagus	oesophagus
44	chr10:98603200-98606000	Weak transcription	Pancreas	Pancrea
45	chr10:98603200-98606000	Weak transcription	HMEC	breast
46	chr10:98603200-98606800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:98603200-98606800	Weak transcription	Left Ventricle	heart
48	chr10:98603200-98610200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:98603200-98610200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:98603200-98610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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