Variant report

Variant	rs11124685
Chromosome Location	chr2:39741928-39741929
allele	C/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	TEAD4	chr2:39741859-39744517	HepG2	liver:	n/a	n/a
2	CTCF	chr2:39740528-39742023	SK-N-SH	brain:	n/a	chr2:39740968-39740984 chr2:39740970-39740983 chr2:39740967-39740985 chr2:39740970-39740979
3	GATA3	chr2:39741794-39741965	SH-SY5Y	brain:	n/a	n/a
4	GATA1	chr2:39738273-39741947	K562	blood:	n/a	chr2:39739122-39739135 chr2:39739125-39739142 chr2:39740191-39740199 chr2:39739123-39739133 chr2:39741274-39741281 chr2:39739124-39739133 chr2:39738906-39738915 chr2:39739124-39739131 chr2:39739075-39739096 chr2:39738948-39738958
5	RAD21	chr2:39740568-39742169	SK-N-SH	brain:	n/a	chr2:39740968-39740987

No.	Distal block	Cell Line	Cell type
1	chr2:39662739..39665168-chr2:39741315..39743608,2	K562	blood:
2	chr2:39661305..39663930-chr2:39740460..39742003,2	MCF-7	breast:
3	chr2:39741394..39743199-chr2:39794476..39796005,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39741287-39742486	ENSG00000231312.2

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11124684	0.80[EUR][1000 genomes]
rs11124686	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11680511	0.81[AMR][1000 genomes]
rs11891871	0.81[EUR][1000 genomes]
rs1526024	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1997113	0.85[CEU][hapmap]
rs2287089	0.80[EUR][1000 genomes]
rs6741839	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6753798	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7577879	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs7585512	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7591326	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39712400-39748600	Weak transcription	Aorta	Aorta
2	chr2:39724800-39750600	Weak transcription	Gastric	stomach
3	chr2:39733000-39743600	Weak transcription	Hela-S3	cervix
4	chr2:39734600-39745000	Enhancers	Adipose Nuclei	Adipose
5	chr2:39734600-39746000	Enhancers	Fetal Heart	heart
6	chr2:39735000-39744800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:39736400-39742000	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:39736400-39745000	Enhancers	Right Atrium	heart
9	chr2:39736400-39745000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:39737000-39744800	Enhancers	Fetal Muscle Leg	muscle
11	chr2:39737000-39745000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39737400-39743000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:39738000-39745000	Enhancers	Duodenum Mucosa	Duodenum
14	chr2:39738400-39742000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:39738800-39743000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:39738800-39743000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:39739400-39743600	Enhancers	HUVEC	blood vessel
18	chr2:39739600-39742600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:39739600-39742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:39739600-39743200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:39739800-39742600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:39739800-39742600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:39739800-39743400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:39739800-39744200	Enhancers	K562	blood
25	chr2:39739800-39745600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr2:39740200-39743600	Weak transcription	Fetal Brain Male	brain
27	chr2:39740400-39742400	Weak transcription	Fetal Intestine Large	intestine
28	chr2:39740600-39745000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr2:39740800-39742200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:39740800-39742600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:39740800-39742800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:39740800-39743400	Enhancers	Lung	lung
33	chr2:39740800-39745000	Enhancers	Left Ventricle	heart
34	chr2:39741000-39742600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:39741200-39742400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:39741200-39742600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:39741200-39742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:39741200-39743400	Weak transcription	Small Intestine	intestine
39	chr2:39741200-39743800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:39741400-39742400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:39741400-39742400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:39741400-39742400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:39741400-39742400	Weak transcription	Fetal Stomach	stomach
44	chr2:39741400-39742600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr2:39741400-39742600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:39741400-39742600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:39741400-39742600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:39741400-39742600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:39741400-39742600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:39741400-39742600	Weak transcription	Rectal Smooth Muscle	rectum

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