Variant report

Variant	rs12529910
Chromosome Location	chr6:2241204-2241205
allele	C/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	STAT3	chr6:2241067-2241255	MCF10A-Er-Src	breast:	n/a	n/a
2	USF2	chr6:2241187-2241386	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:2232725..2235057-chr6:2241129..2244021,2	MCF-7	breast:
2	chr6:2240186..2242640-chr6:2244127..2247003,3	K562	blood:
3	chr6:2239411..2242031-chr6:2243172..2247003,4	K562	blood:
4	chr6:2239677..2242636-chr6:2266215..2268461,2	K562	blood:

Variant related genes	Relation type
GMDS-AS1	TF binding region
ENSG00000250903	Chromatin interaction
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1196389	0.81[JPT][hapmap]
rs2479015	0.86[JPT][hapmap]
rs335963	0.86[JPT][hapmap]
rs3800186	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9328086	0.86[JPT][hapmap]
rs9378691	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
18	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2222600-2244400	Weak transcription	Fetal Stomach	stomach
2	chr6:2222600-2244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:2222800-2243800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:2228600-2243800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:2231600-2243200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:2231600-2243800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:2231800-2242600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:2231800-2244200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:2232000-2244800	Weak transcription	Aorta	Aorta
10	chr6:2233200-2244000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:2233400-2244400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:2233400-2244400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:2233400-2244600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:2236600-2244200	Weak transcription	Pancreas	Pancrea
15	chr6:2236800-2243200	Weak transcription	Gastric	stomach
16	chr6:2237600-2244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:2237600-2244600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:2237600-2244600	Weak transcription	Fetal Brain Female	brain
19	chr6:2237800-2244400	Weak transcription	NHEK	skin
20	chr6:2237800-2244800	Weak transcription	NHLF	lung
21	chr6:2238200-2244600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:2238400-2242400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:2238400-2243200	Weak transcription	Hela-S3	cervix
24	chr6:2238400-2243800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:2238400-2243800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:2238400-2244400	Weak transcription	HMEC	breast
27	chr6:2238400-2244400	Weak transcription	Osteobl	bone
28	chr6:2238400-2245000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:2239400-2241400	Enhancers	Fetal Intestine Large	intestine
30	chr6:2239800-2241400	Enhancers	Small Intestine	intestine
31	chr6:2239800-2241600	Enhancers	Fetal Intestine Small	intestine
32	chr6:2239800-2242800	Enhancers	Stomach Mucosa	stomach
33	chr6:2240200-2244200	Weak transcription	Primary B cells from cord blood	blood
34	chr6:2240600-2241600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:2241000-2241800	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr6:2241000-2242200	Enhancers	GM12878-XiMat	blood
37	chr6:2241000-2243400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr6:2241000-2243400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:2241200-2241400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr6:2241200-2241400	Enhancers	Psoas Muscle	Psoas
41	chr6:2241200-2241600	Enhancers	Colonic Mucosa	Colon
42	chr6:2241200-2241800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:2241200-2241800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:2241200-2241800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:2241200-2242200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:2241200-2242200	Transcr. at gene 5' and 3'	HepG2	liver
47	chr6:2241200-2242600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:2241200-2242800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:2241200-2242800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:2241200-2243600	Enhancers	HUES64 Cell Line	embryonic stem cell

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