Variant report

Variant	rs62010170
Chromosome Location	chr15:83709325-83709326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83709236-83709489	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:83668024..83670019-chr15:83707664..83709687,2	K562	blood:
2	chr15:83679479..83681361-chr15:83707493..83709575,2	MCF-7	breast:
3	chr15:83706535..83711494-chr15:83875161..83878411,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259308	TF binding region
ENSG00000166503	Chromatin interaction
ENSG00000169609	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1010820	0.82[EUR][1000 genomes]
rs10520576	0.82[EUR][1000 genomes]
rs1075619	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112404	0.82[EUR][1000 genomes]
rs11259965	0.82[EUR][1000 genomes]
rs11259968	0.82[EUR][1000 genomes]
rs11259970	0.82[EUR][1000 genomes]
rs11852408	0.82[EUR][1000 genomes]
rs11852446	0.82[EUR][1000 genomes]
rs11853498	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.82[EUR][1000 genomes]
rs11855639	0.82[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.82[EUR][1000 genomes]
rs11857428	0.84[EUR][1000 genomes]
rs11857641	0.81[EUR][1000 genomes]
rs11858162	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	0.84[EUR][1000 genomes]
rs11858468	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437558	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12437901	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.82[EUR][1000 genomes]
rs12438575	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439122	1.00[ASN][1000 genomes]
rs12439903	0.82[EUR][1000 genomes]
rs12440265	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440386	0.84[EUR][1000 genomes]
rs12440562	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441006	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.82[EUR][1000 genomes]
rs12441907	1.00[ASN][1000 genomes]
rs12443109	0.82[EUR][1000 genomes]
rs12443424	0.82[EUR][1000 genomes]
rs12591855	0.82[EUR][1000 genomes]
rs12593532	0.82[EUR][1000 genomes]
rs12595330	0.82[EUR][1000 genomes]
rs17361375	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.83[EUR][1000 genomes]
rs17507763	0.83[EUR][1000 genomes]
rs17508610	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	0.81[EUR][1000 genomes]
rs17568298	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	0.82[EUR][1000 genomes]
rs2034618	0.83[EUR][1000 genomes]
rs4300612	1.00[ASN][1000 genomes]
rs4408505	1.00[ASN][1000 genomes]
rs4423388	1.00[ASN][1000 genomes]
rs4480763	1.00[ASN][1000 genomes]
rs4547301	1.00[ASN][1000 genomes]
rs4563011	0.81[EUR][1000 genomes]
rs4572349	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683536	0.82[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55756182	1.00[ASN][1000 genomes]
rs55878453	1.00[ASN][1000 genomes]
rs55893521	1.00[ASN][1000 genomes]
rs55932429	1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs56045305	0.82[EUR][1000 genomes]
rs56052029	0.81[EUR][1000 genomes]
rs56352317	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.82[EUR][1000 genomes]
rs57729044	0.82[EUR][1000 genomes]
rs58006707	0.82[EUR][1000 genomes]
rs58281154	0.82[EUR][1000 genomes]
rs58396076	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59896565	0.82[EUR][1000 genomes]
rs60344060	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010162	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010164	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010172	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010173	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.83[EUR][1000 genomes]
rs62010214	0.81[EUR][1000 genomes]
rs62010215	0.82[EUR][1000 genomes]
rs62010220	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.82[EUR][1000 genomes]
rs62010252	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.82[EUR][1000 genomes]
rs62010258	0.82[EUR][1000 genomes]
rs62011742	0.84[EUR][1000 genomes]
rs62011744	0.87[EUR][1000 genomes]
rs62011869	0.84[EUR][1000 genomes]
rs62025914	1.00[ASN][1000 genomes]
rs62025915	1.00[ASN][1000 genomes]
rs6603042	1.00[ASN][1000 genomes]
rs66619192	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67022650	0.84[EUR][1000 genomes]
rs67933024	1.00[ASN][1000 genomes]
rs7164083	0.82[EUR][1000 genomes]
rs7165114	0.82[EUR][1000 genomes]
rs7165978	0.82[EUR][1000 genomes]
rs7172590	1.00[ASN][1000 genomes]
rs7179675	1.00[ASN][1000 genomes]
rs7180692	1.00[ASN][1000 genomes]
rs72755992	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	0.82[EUR][1000 genomes]
rs8027577	0.82[EUR][1000 genomes]
rs8031723	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033380	1.00[ASN][1000 genomes]
rs8035852	0.97[AFR][1000 genomes]
rs8038486	0.82[EUR][1000 genomes]
rs8043224	0.84[EUR][1000 genomes]
rs965263	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	0.82[EUR][1000 genomes]
rs9707895	0.81[EUR][1000 genomes];1.00[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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
3	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain
6	chr15:83695400-83714600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:83695800-83715400	Weak transcription	HSMMtube	muscle
8	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
9	chr15:83698600-83709600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:83698800-83712000	Weak transcription	Colonic Mucosa	Colon
11	chr15:83699000-83710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:83699000-83712000	Weak transcription	Gastric	stomach
13	chr15:83699000-83715800	Weak transcription	Brain Substantia Nigra	brain
14	chr15:83699000-83716800	Weak transcription	Aorta	Aorta
15	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:83704800-83710800	Strong transcription	Primary B cells from cord blood	blood
19	chr15:83705000-83710600	Strong transcription	K562	blood
20	chr15:83705000-83720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:83705000-83725800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:83705200-83715000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:83705200-83720000	Strong transcription	Dnd41	blood
25	chr15:83705600-83711000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:83705600-83712200	Weak transcription	NHDF-Ad	bronchial
27	chr15:83705600-83714400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:83705600-83721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:83705800-83710800	Strong transcription	Primary T cells from cord blood	blood
30	chr15:83706000-83725400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:83706200-83711000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:83706600-83710600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:83706600-83718000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:83706800-83712600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:83706800-83713400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:83707000-83710600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:83707000-83725400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:83707200-83710600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr15:83707200-83710600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:83707400-83710600	Strong transcription	Brain Hippocampus Middle	brain
42	chr15:83707400-83710600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr15:83707400-83712600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:83707400-83712800	Strong transcription	HepG2	liver
45	chr15:83707400-83713000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:83707400-83713400	Strong transcription	Fetal Thymus	thymus
47	chr15:83707400-83718400	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:83707400-83725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:83707800-83719200	Strong transcription	GM12878-XiMat	blood
50	chr15:83708000-83710000	Strong transcription	Brain Germinal Matrix	brain

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