Variant report

Variant	rs3740573
Chromosome Location	chr10:118032625-118032626
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	CTCF	chr10:118032500-118032650	HRE	kidney:	n/a	n/a
2	CTCF	chr10:118032480-118032630	HFF-Myc	foreskin:	n/a	n/a
3	MAZ	chr10:118031041-118033880	IMR90	lung:	n/a	chr10:118032586-118032596 chr10:118033682-118033691 chr10:118033306-118033315 chr10:118032757-118032767
4	BACH1	chr10:118032561-118032688	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr10:118032514-118033280	H1-hESC	embryonic stem cell:	n/a	chr10:118032753-118032765 chr10:118032756-118032765
6	CTCF	chr10:118032500-118032650	AG04449	skin:	n/a	n/a
7	CTCF	chr10:118032620-118032770	NHDF-neo	bronchial:	n/a	n/a
8	SIN3A	chr10:118030376-118033421	H1-hESC	embryonic stem cell:	n/a	chr10:118033014-118033023 chr10:118033126-118033139 chr10:118033136-118033145 chr10:118030632-118030643 chr10:118033006-118033017
9	CTCF	chr10:118032580-118032730	MCF-7	breast:	n/a	n/a
10	CTCF	chr10:118032540-118032690	HBMEC	blood vessel:	n/a	n/a
11	CTCF	chr10:118032480-118032630	GM12864	blood:	n/a	n/a
12	MAX	chr10:118031480-118034385	A549	lung:	n/a	chr10:118032586-118032596 chr10:118034183-118034199 chr10:118033682-118033691 chr10:118033306-118033315 chr10:118032757-118032767
13	POLR2A	chr10:118031413-118032774	MCF-7	breast:	n/a	n/a
14	HA-E2F1	chr10:118031428-118033422	MCF-7	breast:	n/a	chr10:118031794-118031808 chr10:118032753-118032765 chr10:118032756-118032765
15	POLR2A	chr10:118031272-118034347	MCF-7	breast:	n/a	n/a
16	CTCF	chr10:118032502-118032665	IMR90	lung:	n/a	n/a
17	CTCF	chr10:118032520-118032670	HEK293	kidney:	n/a	n/a
18	CTCF	chr10:118032480-118032630	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr10:118032520-118032670	BJ	skin:	n/a	n/a
20	CTCF	chr10:118032520-118032670	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr10:118032480-118032630	HRPEpiC	eye:	n/a	n/a
22	POLR2A	chr10:118022229-118034776	MCF-7	breast:	n/a	n/a
23	ZNF263	chr10:118031708-118034525	HEK293-T-REx	kidney:	n/a	chr10:118034011-118034020 chr10:118032764-118032773 chr10:118034005-118034026 chr10:118034014-118034023
24	POLR2A	chr10:118032505-118033854	H1-neurons	neurons:	n/a	n/a
25	SIN3AK20	chr10:118029149-118034735	MCF-7	breast:	n/a	n/a
26	FOXA2	chr10:118032384-118033022	A549	lung:	n/a	chr10:118032715-118032727 chr10:118032719-118032731
27	ZNF143	chr10:118031956-118032959	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTBP2	chr10:118030332-118033128	H1-hESC	embryonic stem cell:	n/a	n/a
29	FOXA2	chr10:118032514-118032880	A549	lung:	n/a	chr10:118032715-118032727 chr10:118032719-118032731
30	CHD1	chr10:118031968-118033015	H1-hESC	embryonic stem cell:	n/a	chr10:118032701-118032711
31	TCF12	chr10:118032371-118032845	A549	lung:	n/a	n/a
32	YY1	chr10:118032466-118033549	H1-hESC	embryonic stem cell:	n/a	chr10:118032473-118032487 chr10:118032756-118032765 chr10:118033132-118033146
33	RAD21	chr10:118032062-118032781	H1-hESC	embryonic stem cell:	n/a	chr10:118032302-118032315

Variant related genes	Relation type
GFRA1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11197615	0.95[ASN][1000 genomes]
rs11816383	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11817803	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12414617	0.80[AMR][1000 genomes]
rs12414695	0.88[EUR][1000 genomes]
rs12416076	0.85[AMR][1000 genomes]
rs12416567	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1362216	0.92[EUR][1000 genomes]
rs1419876	0.88[EUR][1000 genomes]
rs17094490	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17094504	0.83[AMR][1000 genomes]
rs17094520	0.85[AMR][1000 genomes]
rs2074986	0.92[EUR][1000 genomes]
rs2286630	0.85[AMR][1000 genomes]
rs2438177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2532687	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2532688	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2577362	0.92[EUR][1000 genomes]
rs35997739	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41386650	0.85[AMR][1000 genomes]
rs4320877	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61092077	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7092496	0.92[EUR][1000 genomes]
rs73371096	0.88[EUR][1000 genomes]
rs73373010	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73373021	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73373031	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8192661	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449389	chr10:117806874-118102404	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832000	chr10:117944492-118116253	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3332511	chr10:118030012-118035110	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:118029600-118034200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr10:118029800-118032800	Active TSS	Fetal Kidney	kidney
3	chr10:118030000-118034200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr10:118030000-118034400	Active TSS	Rectal Smooth Muscle	rectum
5	chr10:118030000-118034600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
6	chr10:118030200-118033800	Active TSS	HSMM	muscle
7	chr10:118030200-118033800	Active TSS	HSMMtube	muscle
8	chr10:118030200-118034000	Active TSS	Muscle Satellite Cultured Cells	--
9	chr10:118030200-118034200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr10:118030200-118034200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:118030200-118034400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:118030200-118034400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr10:118030200-118034400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr10:118030200-118034400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
15	chr10:118030200-118034600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr10:118030400-118032800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:118030400-118033200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr10:118030400-118033400	Active TSS	Brain Angular Gyrus	brain
19	chr10:118030400-118033800	Bivalent/Poised TSS	Left Ventricle	heart
20	chr10:118030400-118034200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:118030400-118034200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr10:118030400-118034200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:118030400-118034200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:118030400-118034200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:118030400-118034400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr10:118030400-118034600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:118030600-118033200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:118030600-118034000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr10:118030600-118034200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:118030600-118034200	Active TSS	Ovary	ovary
31	chr10:118030600-118034400	Active TSS	Right Atrium	heart
32	chr10:118030600-118034600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr10:118030800-118033000	Bivalent/Poised TSS	NH-A	brain
34	chr10:118030800-118033800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr10:118030800-118034000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr10:118030800-118034200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr10:118030800-118034200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:118030800-118034200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:118030800-118034200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:118030800-118034200	Bivalent/Poised TSS	Thymus	Thymus
41	chr10:118030800-118034400	Active TSS	Aorta	Aorta
42	chr10:118030800-118034400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
43	chr10:118031000-118032800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr10:118031000-118033000	Active TSS	Psoas Muscle	Psoas
45	chr10:118031000-118033000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
46	chr10:118031000-118033400	Bivalent/Poised TSS	Fetal Thymus	thymus
47	chr10:118031000-118034000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr10:118031000-118034200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:118031000-118034400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:118031000-118034400	Bivalent/Poised TSS	A549	lung

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