Variant report

Variant	rs2982229
Chromosome Location	chr10:43048841-43048842
allele	G/T
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	MAX	chr10:43047356-43048854	ECC-1	luminal epithelium:	n/a	n/a
2	GABPA	chr10:43047790-43048927	MCF-7	breast:	n/a	n/a
3	KAP1	chr10:43047250-43048854	HEK293	kidney:	n/a	n/a
4	ZNF143	chr10:43047753-43048852	K562	blood:	n/a	chr10:43048570-43048579
5	ARID3A	chr10:43048220-43048891	HepG2	liver:	n/a	n/a
6	HCFC1	chr10:43047619-43049009	Hela-S3	cervix:	n/a	n/a
7	MAX	chr10:43047347-43048867	A549	lung:	n/a	n/a
8	MAX	chr10:43047225-43048899	HepG2	liver:	n/a	n/a
9	RCOR1	chr10:43047437-43048893	GM12878	blood:	n/a	n/a
10	ELF1	chr10:43047303-43048874	GM12878	blood:	n/a	chr10:43048602-43048613
11	ZNF143	chr10:43047633-43048856	GM12878	blood:	n/a	chr10:43048570-43048579
12	MAX	chr10:43048074-43048869	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr10:43047206-43049183	HepG2	liver:	n/a	n/a
14	MAX	chr10:43047234-43048898	A549	lung:	n/a	n/a
15	NRF1	chr10:43047963-43048920	SK-N-SH	brain:	n/a	chr10:43048260-43048271
16	MAX	chr10:43047307-43048863	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43046301..43049301-chr10:43278095..43279962,3	K562	blood:
2	chr10:43043951..43049889-chr10:43132519..43135803,5	K562	blood:
3	chr10:43048254..43049868-chr10:43050241..43052640,2	K562	blood:

Variant related genes	Relation type
ZNF37BP	TF binding region
FXYD6P1	TF binding region
ENSG00000270762	Chromatin interaction
ENSG00000196693	Chromatin interaction
ENSG00000272373	Chromatin interaction
ENSG00000165733	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1255366	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255367	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255368	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1255371	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1255372	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1255403	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1255405	0.87[EUR][1000 genomes]
rs1255407	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs158373	0.80[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs158376	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs158377	1.00[YRI][hapmap]
rs158378	1.00[YRI][hapmap]
rs158382	0.88[YRI][hapmap]
rs158389	0.80[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs158391	1.00[YRI][hapmap]
rs158392	0.80[CEU][hapmap]
rs1760687	0.84[CHB][hapmap]
rs210219	1.00[YRI][hapmap]
rs210224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs210232	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs210233	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210235	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210237	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs210242	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs210253	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210258	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210261	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210262	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210272	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs210278	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs210279	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs210284	0.88[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs210287	0.80[AMR][1000 genomes]
rs2484298	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2801951	0.82[TSI][hapmap]
rs289183	0.80[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap]
rs504191	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550670	chr10:42725663-43089965	Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv895054	chr10:42761931-43068841	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv466877	chr10:42794125-43066414	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv550683	chr10:42794125-43066414	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv895071	chr10:42864138-43066414	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv895073	chr10:42884169-43066505	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
15	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv8625	chr10:43046814-43052296	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv948327	chr10:43048798-43051168	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2982229	CCNYL2	cis	Artery Aorta	GTEx
rs2982229	LINC00839	cis	Artery Aorta	GTEx
rs2982229	LINC00839	cis	Esophagus Mucosa	GTEx
rs2982229	LINC00839	cis	lung	GTEx
rs2982229	LINC00839	cis	Nerve Tibial	GTEx
rs2982229	LOC84856	cis	parietal	SCAN
rs2982229	LINC00839	cis	Esophagus Muscularis	GTEx
rs2982229	BMS1	cis	cerebellum	SCAN
rs2982229	LINC00839	cis	Artery Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43047000-43049000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr10:43047000-43049000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr10:43047000-43049000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:43047000-43049200	Active TSS	Fetal Kidney	kidney
5	chr10:43047000-43049200	Active TSS	A549	lung
6	chr10:43047200-43049000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:43047200-43049000	Active TSS	Fetal Intestine Small	intestine
8	chr10:43047200-43049000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr10:43047400-43049000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr10:43047400-43049000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:43047400-43049000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr10:43047400-43049000	Active TSS	HSMMtube	muscle
13	chr10:43047600-43049000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:43047600-43049000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:43047600-43049000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:43047600-43049000	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr10:43047600-43049000	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr10:43047600-43049000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:43047600-43049000	Active TSS	Aorta	Aorta
20	chr10:43047600-43049000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:43047600-43049000	Active TSS	Brain Substantia Nigra	brain
22	chr10:43047600-43049000	Active TSS	Fetal Intestine Large	intestine
23	chr10:43047600-43049000	Active TSS	Fetal Stomach	stomach
24	chr10:43047600-43049000	Active TSS	Ovary	ovary
25	chr10:43047600-43049000	Active TSS	Psoas Muscle	Psoas
26	chr10:43047600-43049000	Active TSS	Right Atrium	heart
27	chr10:43047600-43049000	Active TSS	Right Ventricle	heart
28	chr10:43047600-43049000	Active TSS	Stomach Mucosa	stomach
29	chr10:43047600-43049000	Active TSS	Thymus	Thymus
30	chr10:43047600-43049000	Active TSS	Osteobl	bone
31	chr10:43047600-43049200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr10:43047600-43049200	Active TSS	NHDF-Ad	bronchial
33	chr10:43047800-43049000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr10:43047800-43049000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:43047800-43049000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr10:43047800-43049000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr10:43047800-43049000	Active TSS	Muscle Satellite Cultured Cells	--
38	chr10:43047800-43049000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:43047800-43049000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr10:43047800-43049000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:43047800-43049000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:43047800-43049000	Active TSS	Brain Angular Gyrus	brain
43	chr10:43047800-43049000	Active TSS	Colonic Mucosa	Colon
44	chr10:43047800-43049000	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr10:43047800-43049000	Active TSS	Fetal Brain Male	brain
46	chr10:43047800-43049000	Active TSS	Fetal Thymus	thymus
47	chr10:43047800-43049000	Active TSS	GM12878-XiMat	blood
48	chr10:43047800-43049200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:43047800-43049200	Active TSS	Brain Germinal Matrix	brain
50	chr10:43047800-43049200	Active TSS	Brain Inferior Temporal Lobe	brain

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