Variant report

Variant	rs1892394
Chromosome Location	chr10:28379138-28379139
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28364402..28367665-chr10:28377622..28380231,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10047289	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10453982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10763639	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10763640	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10763642	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10763644	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10826394	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10826395	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10826400	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10826402	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11006821	0.81[CEU][hapmap]
rs11006822	0.81[CEU][hapmap]
rs11006830	0.90[CEU][hapmap]
rs11006847	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11006851	0.86[EUR][1000 genomes]
rs11006852	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006861	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11006868	0.82[JPT][hapmap]
rs12253376	0.90[CEU][hapmap]
rs1574418	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928644	0.82[JPT][hapmap]
rs2069202	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs3802520	0.90[CEU][hapmap]
rs3885634	0.90[CEU][hapmap]
rs4333922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4336934	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4399242	0.86[EUR][1000 genomes]
rs4749301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6481499	0.90[CEU][hapmap]
rs7091158	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7474568	0.89[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7478224	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7478236	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7478252	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7478268	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7894339	0.85[EUR][1000 genomes]
rs7897848	0.83[EUR][1000 genomes]
rs7898270	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7898446	0.86[EUR][1000 genomes]
rs7898482	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7903192	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7914592	0.86[EUR][1000 genomes]
rs7916852	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7920296	0.82[JPT][hapmap]
rs7920402	0.82[JPT][hapmap]
rs7923978	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv831815	chr10:28235661-28407533	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv894988	chr10:28337570-28410989	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv466855	chr10:28341783-28400835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv550284	chr10:28341783-28400835	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1817535	chr10:28373644-28409054	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1848511	chr10:28373644-28464753	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28347000-28380400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr10:28347000-28381000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr10:28347000-28412200	Weak transcription	Left Ventricle	heart
4	chr10:28347000-28414600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:28348000-28381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:28357200-28380200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:28364800-28379600	Weak transcription	Adipose Nuclei	Adipose
8	chr10:28364800-28392000	Weak transcription	Gastric	stomach
9	chr10:28364800-28416600	Weak transcription	Pancreas	Pancrea
10	chr10:28365000-28379600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:28365200-28379600	Weak transcription	HepG2	liver
12	chr10:28365200-28380200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr10:28367800-28420200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:28371400-28379800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:28373400-28379600	Weak transcription	Lung	lung
16	chr10:28375400-28379200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr10:28375600-28379200	Strong transcription	Aorta	Aorta
18	chr10:28375600-28380000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:28376000-28379200	Strong transcription	Fetal Intestine Small	intestine
20	chr10:28376000-28438400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr10:28376600-28379200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:28376600-28379200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr10:28376600-28382200	Enhancers	HUVEC	blood vessel
24	chr10:28376600-28416600	Weak transcription	Fetal Intestine Large	intestine
25	chr10:28376800-28392000	Weak transcription	Esophagus	oesophagus
26	chr10:28377400-28379200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr10:28377400-28379200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr10:28377400-28379800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr10:28377600-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:28377800-28388200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:28378000-28379200	Enhancers	Osteobl	bone
32	chr10:28378000-28418400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr10:28378200-28379200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:28378200-28379800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:28378200-28380200	Weak transcription	Fetal Stomach	stomach
36	chr10:28378400-28381200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:28378400-28386400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr10:28378600-28380200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:28378600-28396200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr10:28378600-28400800	Weak transcription	HSMM	muscle
41	chr10:28378600-28407400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr10:28378600-28412800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:28378600-28425600	Weak transcription	Colon Smooth Muscle	Colon
44	chr10:28378800-28379200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:28378800-28379600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:28378800-28380600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:28378800-28382800	Weak transcription	Primary T cells from cord blood	blood
48	chr10:28378800-28396400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr10:28378800-28407400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr10:28378800-28408400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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