Variant report

Variant	rs3802378
Chromosome Location	chr9:94538200-94538201
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	RAD21	chr9:94537332-94539151	SK-N-SH	brain:	n/a	chr9:94537897-94537916 chr9:94538475-94538494 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94538235-94538254 chr9:94537900-94537913
2	CTCF	chr9:94538160-94538310	NHEK	skin:	n/a	n/a
3	RAD21	chr9:94537614-94538261	MCF-7	breast:	n/a	chr9:94537897-94537916 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94538235-94538254 chr9:94537900-94537913
4	RAD21	chr9:94537595-94538223	H1-hESC	embryonic stem cell:	n/a	chr9:94537897-94537916 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94537900-94537913
5	SMC3	chr9:94537473-94538676	SK-N-SH	brain:	n/a	chr9:94537898-94537906 chr9:94537898-94537912 chr9:94537902-94537912
6	MAZ	chr9:94537657-94538276	IMR90	lung:	n/a	n/a
7	MYC	chr9:94537711-94538265	A549	lung:	n/a	n/a
8	CTCF	chr9:94537643-94538308	A549	lung:	n/a	chr9:94537899-94537912 chr9:94537901-94537911 chr9:94537897-94537913 chr9:94537896-94537914 chr9:94537899-94537908 chr9:94537898-94537919
9	CTCF	chr9:94537516-94538445	HCT-116	colon:	n/a	chr9:94537899-94537912 chr9:94537901-94537911 chr9:94537897-94537913 chr9:94537896-94537914 chr9:94537899-94537908 chr9:94537898-94537919
10	CTCF	chr9:94537177-94538312	SK-N-SH	brain:	n/a	chr9:94537899-94537912 chr9:94537901-94537911 chr9:94537897-94537913 chr9:94537896-94537914 chr9:94537899-94537908 chr9:94537898-94537919
11	RAD21	chr9:94537521-94538297	HCT-116	colon:	n/a	chr9:94537897-94537916 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94538235-94538254 chr9:94537900-94537913
12	RAD21	chr9:94537672-94538229	ECC-1	luminal epithelium:	n/a	chr9:94537897-94537916 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94537900-94537913
13	RAD21	chr9:94537524-94538252	HCT-116	colon:	n/a	chr9:94537897-94537916 chr9:94537902-94537914 chr9:94537902-94537912 chr9:94537900-94537913
14	CTCF	chr9:94537556-94538218	MCF-7	breast:	n/a	chr9:94537899-94537912 chr9:94537901-94537911 chr9:94537897-94537913 chr9:94537896-94537914 chr9:94537899-94537908 chr9:94537898-94537919

No.	Distal block	Cell Line	Cell type
1	chr9:94537481..94538450-chr9:94712230..94712819,2	MCF-7	breast:
2	chr9:94537447..94538880-chr9:94712081..94713098,9	MCF-7	breast:
3	chr9:94537694..94538378-chr9:94712239..94713033,2	K562	blood:
4	chr10:131265189..131266009-chr9:94537721..94538470,2	HCT-116	colon:
5	chr9:94538158..94540180-chr9:94661146..94663275,2	K562	blood:

Variant related genes	Relation type
ROR2	TF binding region
ENSG00000169071	Chromatin interaction
ENSG00000170430	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10512217	0.82[YRI][hapmap]
rs10820902	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10820903	0.81[AMR][1000 genomes]
rs10992086	0.87[MKK][hapmap];0.91[YRI][hapmap]
rs10992087	0.81[MKK][hapmap]
rs10992090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992104	0.83[AMR][1000 genomes]
rs10992108	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10992109	0.83[AMR][1000 genomes]
rs12237459	0.91[YRI][hapmap]
rs12237573	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238428	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12685213	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs12685849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs16907754	0.82[AFR][1000 genomes]
rs16907761	0.81[MKK][hapmap];0.84[YRI][hapmap]
rs16907764	0.84[MKK][hapmap];0.84[YRI][hapmap]
rs16907768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16907776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178196	0.83[AMR][1000 genomes]
rs2312730	0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3802377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322069	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4398991	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4400454	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4452868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes]
rs4595186	0.91[YRI][hapmap]
rs4601388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57810120	0.93[EUR][1000 genomes]
rs58210546	0.93[EUR][1000 genomes]
rs58462029	0.93[EUR][1000 genomes]
rs60092492	0.93[EUR][1000 genomes]
rs60617711	0.93[EUR][1000 genomes]
rs73511086	0.93[EUR][1000 genomes]
rs73513203	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73513246	0.98[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73651508	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94527600-94538800	Weak transcription	K562	blood
2	chr9:94529400-94539800	Enhancers	Colon Smooth Muscle	Colon
3	chr9:94532200-94539200	Enhancers	Fetal Heart	heart
4	chr9:94533000-94542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:94533000-94543600	Weak transcription	Right Atrium	heart
6	chr9:94533400-94549600	Weak transcription	Colonic Mucosa	Colon
7	chr9:94533600-94545400	Enhancers	Stomach Smooth Muscle	stomach
8	chr9:94534200-94538200	Genic enhancers	Fetal Stomach	stomach
9	chr9:94534400-94546800	Weak transcription	Fetal Kidney	kidney
10	chr9:94534600-94538800	Weak transcription	Spleen	Spleen
11	chr9:94534600-94539400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:94535000-94538600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:94535000-94539400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:94536000-94543200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:94536000-94543600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:94536200-94544600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:94536400-94538400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:94536600-94538800	Weak transcription	Placenta	Placenta
19	chr9:94537000-94543400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:94537200-94539800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr9:94537400-94538200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:94537600-94538200	Enhancers	Fetal Intestine Large	intestine
23	chr9:94537600-94538200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr9:94537600-94538200	Enhancers	Ovary	ovary
25	chr9:94537600-94538600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:94537600-94538800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:94537600-94538800	Enhancers	Fetal Lung	lung
28	chr9:94537600-94539600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:94537800-94538200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:94537800-94538200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr9:94537800-94538200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr9:94537800-94538800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:94537800-94541000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:94537800-94543400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:94537800-94545000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:94537800-94546000	Weak transcription	Gastric	stomach
37	chr9:94538000-94538200	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr9:94538000-94538600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr9:94538000-94538800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:94538000-94538800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr9:94538000-94539400	Enhancers	Rectal Smooth Muscle	rectum
42	chr9:94538000-94540400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:94538000-94540400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:94538000-94540600	Enhancers	NHLF	lung
45	chr9:94538000-94541000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:94538000-94548800	Weak transcription	Esophagus	oesophagus
47	chr9:94538200-94538600	Weak transcription	Ovary	ovary
48	chr9:94538200-94539200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:94538200-94539400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:94538200-94539600	Enhancers	Fetal Stomach	stomach

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