Variant report

Variant	rs61840548
Chromosome Location	chr10:49515736-49515737
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	GATA3	chr10:49515673-49516050	SH-SY5Y	brain:	n/a	chr10:49515797-49515813 chr10:49515795-49515816
2	POLR2A	chr10:49514145-49515974	H1-neurons	neurons:	n/a	n/a
3	RFX5	chr10:49515233-49516077	Hela-S3	cervix:	n/a	n/a
4	UBTF	chr10:49514278-49515881	K562	blood:	n/a	n/a
5	NR2F2	chr10:49515057-49515790	K562	blood:	n/a	chr10:49515535-49515550
6	POLR2A	chr10:49515615-49516160	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr10:49514192-49515870	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr10:49515670-49515830	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr10:49515602-49515754	K562	blood:	n/a	n/a
10	MXI1	chr10:49513707-49516843	SK-N-SH	brain:	n/a	n/a
11	GATA2	chr10:49515366-49515906	SH-SY5Y	brain:	n/a	chr10:49515797-49515813 chr10:49515795-49515816
12	UBTF	chr10:49514268-49515854	K562	blood:	n/a	n/a
13	BHLHE40	chr10:49515192-49515938	K562	blood:	n/a	n/a
14	RCOR1	chr10:49515250-49515741	K562	blood:	n/a	n/a
15	MAZ	chr10:49513778-49516109	IMR90	lung:	n/a	chr10:49514453-49514462 chr10:49514453-49514462 chr10:49514443-49514452 chr10:49514454-49514461 chr10:49515181-49515191
16	POLR2A	chr10:49514303-49515967	HepG2	liver:	n/a	n/a
17	HCFC1	chr10:49513973-49515798	K562	blood:	n/a	n/a
18	NR2F2	chr10:49514062-49515742	MCF-7	breast:	n/a	chr10:49515535-49515550
19	RCOR1	chr10:49514117-49515989	K562	blood:	n/a	n/a
20	POLR2A	chr10:49515234-49516312	K562	blood:	n/a	n/a
21	POLR2A	chr10:49514549-49515904	IMR90	lung:	n/a	n/a
22	NR2F2	chr10:49515143-49515932	K562	blood:	n/a	chr10:49515535-49515550
23	CUX1	chr10:49515732-49515989	K562	blood:	n/a	n/a
24	SIN3A	chr10:49514226-49515886	H1-hESC	embryonic stem cell:	n/a	chr10:49514805-49514818
25	REST	chr10:49513611-49516298	H1-neurons	neurons:	n/a	chr10:49514194-49514204 chr10:49515070-49515083 chr10:49514519-49514539 chr10:49514817-49514830
26	POLR2A	chr10:49515048-49515873	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49514655..49517342-chr10:49637868..49640207,2	K562	blood:
2	chr10:49496582..49501262-chr10:49513244..49517429,4	K562	blood:
3	chr10:49498367..49502317-chr10:49513526..49516072,3	MCF-7	breast:

Variant related genes	Relation type
MAPK8	TF binding region
ENSG00000225482	Chromatin interaction
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17010208	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17010407	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17010430	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17010447	0.92[EUR][1000 genomes]
rs17010454	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17010455	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17697972	0.92[EUR][1000 genomes]
rs1867586	0.84[EUR][1000 genomes]
rs3730160	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3855904	0.80[EUR][1000 genomes]
rs57508520	0.92[EUR][1000 genomes]
rs58676018	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60011276	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60992548	0.92[EUR][1000 genomes]
rs61838668	0.92[EUR][1000 genomes]
rs61838669	0.88[EUR][1000 genomes]
rs61838672	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61838673	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61838677	0.92[EUR][1000 genomes]
rs61838697	0.92[EUR][1000 genomes]
rs61838698	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61838700	0.92[EUR][1000 genomes]
rs61838701	0.92[EUR][1000 genomes]
rs61838703	0.89[EUR][1000 genomes]
rs61838704	0.92[EUR][1000 genomes]
rs61838707	0.84[EUR][1000 genomes]
rs61838708	0.81[EUR][1000 genomes]
rs61840549	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61840550	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61840556	0.80[EUR][1000 genomes]
rs61840558	0.92[EUR][1000 genomes]
rs7089077	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	esv3388984	chr10:49513771-49516519	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
8	esv3449549	chr10:49513996-49515994	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49514000-49515800	Active TSS	Muscle Satellite Cultured Cells	--
2	chr10:49514000-49515800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:49514000-49515800	Active TSS	Colonic Mucosa	Colon
4	chr10:49514000-49515800	Active TSS	Fetal Intestine Small	intestine
5	chr10:49514000-49515800	Active TSS	HSMMtube	muscle
6	chr10:49514000-49516200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr10:49514000-49516200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:49514000-49516200	Active TSS	Brain Germinal Matrix	brain
9	chr10:49514000-49516400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:49514000-49516400	Active TSS	Fetal Muscle Trunk	muscle
11	chr10:49514200-49515800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:49514200-49515800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr10:49514200-49515800	Active TSS	Aorta	Aorta
14	chr10:49514200-49515800	Active TSS	NH-A	brain
15	chr10:49514200-49516000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:49514200-49516000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:49514200-49516000	Active TSS	Left Ventricle	heart
18	chr10:49514200-49516200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr10:49514200-49516200	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr10:49514200-49516200	Active TSS	Right Ventricle	heart
21	chr10:49514200-49516400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:49514200-49516400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr10:49514200-49516600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr10:49514200-49516600	Active TSS	Ovary	ovary
25	chr10:49514200-49516600	Active TSS	Psoas Muscle	Psoas
26	chr10:49514200-49516800	Active TSS	Fetal Brain Female	brain
27	chr10:49514400-49515800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:49514400-49515800	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr10:49514400-49515800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr10:49514400-49515800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr10:49514400-49515800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:49514400-49515800	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr10:49514400-49515800	Active TSS	NHDF-Ad	bronchial
34	chr10:49514400-49516000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:49514400-49516000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr10:49514400-49516000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:49514400-49516000	Active TSS	Fetal Stomach	stomach
38	chr10:49514400-49516000	Active TSS	HSMM	muscle
39	chr10:49514400-49516200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr10:49514400-49516200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:49514400-49516200	Active TSS	NHLF	lung
42	chr10:49514400-49516400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:49514400-49516400	Active TSS	NHEK	skin
44	chr10:49514400-49516600	Active TSS	A549	lung
45	chr10:49514600-49515800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:49514600-49516000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr10:49514600-49516000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:49514600-49516000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:49514800-49516000	Active TSS	Right Atrium	heart
50	chr10:49514800-49516400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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