Variant report

Variant	rs4743138
Chromosome Location	chr9:100614296-100614297
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	chr9:100613782-100614557	H1-neurons	neurons:	n/a	n/a
2	CTBP2	chr9:100613864-100616060	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr9:100613856-100618340	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr9:100612750-100618219	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
FOXE1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10116976	1.00[CHB][hapmap]
rs10123699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10739513	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759960	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10760011	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10760017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10983975	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13287360	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1348386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1465965	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1867279	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1912998	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3021523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6478423	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7024345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7046645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7048394	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7848950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7849497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7859751	0.96[CEU][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs7870540	0.81[AMR][1000 genomes]
rs7870795	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs7870871	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs894672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs907576	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs907578	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907579	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907580	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907582	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs925485	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs925486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs925487	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs973473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743138	TMOD1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100613400-100615400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:100613400-100615600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr9:100613400-100615600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
4	chr9:100613400-100615600	Bivalent Enhancer	Spleen	Spleen
5	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:100613600-100615000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr9:100613600-100615200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:100613800-100614400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
12	chr9:100613800-100614600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:100613800-100614600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:100613800-100614800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:100613800-100615200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr9:100613800-100615400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
17	chr9:100613800-100615600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr9:100613800-100615600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
19	chr9:100613800-100615800	Bivalent Enhancer	Fetal Intestine Large	intestine
20	chr9:100613800-100616200	Bivalent Enhancer	Liver	Liver
21	chr9:100613800-100616400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr9:100613800-100616400	Bivalent Enhancer	Fetal Stomach	stomach
25	chr9:100613800-100616600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:100613800-100616800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr9:100613800-100617400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr9:100613800-100617800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr9:100614000-100614400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr9:100614000-100614400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:100614000-100614400	Bivalent/Poised TSS	HSMM	muscle
32	chr9:100614000-100614600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:100614000-100614800	Bivalent Enhancer	Right Ventricle	heart
34	chr9:100614000-100615000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr9:100614000-100615000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:100614000-100615000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:100614000-100615400	Enhancers	Pancreas	Pancrea
38	chr9:100614000-100615600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:100614000-100615600	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr9:100614000-100615600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
41	chr9:100614000-100615800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:100614000-100616400	Bivalent Enhancer	Lung	lung
43	chr9:100614000-100616600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr9:100614000-100617800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr9:100614000-100617800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:100614200-100614400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr9:100614200-100614400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:100614200-100614400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:100614200-100614400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:100614200-100614400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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