Variant report

Variant	rs3802614
Chromosome Location	chr10:27045089-27045090
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27034198..27037050-chr10:27043769..27046738,3	K562	blood:
2	chr10:26986152..26987808-chr10:27043588..27046047,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDSS1-4	chr10:27044553-27045476	NONHSAT011861

Variant related genes	Relation type
ENSG00000148459	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10508721	0.90[YRI][hapmap]
rs12413383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12764628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12774231	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12776877	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12779919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780703	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16927334	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17669895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17747961	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17748178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2094150	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182294	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35175791	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35531360	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5010875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5025734	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67940790	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7091364	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092950	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7094825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7920164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26988000-27069600	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:26997600-27054400	Weak transcription	Fetal Brain Male	brain
3	chr10:27011200-27047400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:27021600-27069600	Weak transcription	Esophagus	oesophagus
5	chr10:27023400-27057800	Weak transcription	Gastric	stomach
6	chr10:27023400-27070000	Weak transcription	Pancreas	Pancrea
7	chr10:27024000-27047600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:27024000-27048000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:27024200-27048600	Weak transcription	Fetal Heart	heart
10	chr10:27024800-27048000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:27025000-27054200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:27025600-27069600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:27025800-27068200	Weak transcription	Spleen	Spleen
14	chr10:27025800-27070800	Weak transcription	Aorta	Aorta
15	chr10:27026000-27069600	Weak transcription	Brain Angular Gyrus	brain
16	chr10:27027400-27069400	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:27027800-27069600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:27028200-27068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:27028400-27069800	Weak transcription	NHLF	lung
20	chr10:27028600-27051600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:27028600-27062200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr10:27029600-27051200	Weak transcription	Brain Anterior Caudate	brain
23	chr10:27029800-27069600	Weak transcription	HSMMtube	muscle
24	chr10:27030200-27048400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:27031200-27049600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:27031400-27049800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:27032000-27068200	Weak transcription	Small Intestine	intestine
28	chr10:27032000-27069600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:27032400-27069400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr10:27032400-27069600	Weak transcription	Lung	lung
31	chr10:27032600-27053400	Weak transcription	Left Ventricle	heart
32	chr10:27032600-27069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:27032800-27060600	Weak transcription	Brain Substantia Nigra	brain
34	chr10:27033200-27064000	Weak transcription	HepG2	liver
35	chr10:27033600-27051000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:27033600-27069200	Weak transcription	Psoas Muscle	Psoas
37	chr10:27034000-27056400	Weak transcription	Fetal Brain Female	brain
38	chr10:27034000-27061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:27034000-27069000	Weak transcription	Colonic Mucosa	Colon
40	chr10:27034000-27069600	Weak transcription	Ovary	ovary
41	chr10:27034000-27069800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:27034200-27049800	Weak transcription	Fetal Stomach	stomach
43	chr10:27034400-27069600	Weak transcription	Right Ventricle	heart
44	chr10:27034600-27049200	Weak transcription	Thymus	Thymus
45	chr10:27034600-27057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:27034800-27049400	Weak transcription	Fetal Intestine Small	intestine
47	chr10:27035600-27060400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:27036000-27045400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:27036600-27049800	Weak transcription	Fetal Kidney	kidney
50	chr10:27036600-27053200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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