Variant report

Variant	rs12196438
Chromosome Location	chr6:25334241-25334242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25278959..25280909-chr6:25333300..25336111,2	MCF-7	breast:
2	chr6:25278190..25281411-chr6:25333036..25336793,4	MCF-7	breast:
3	chr6:25270434..25272961-chr6:25332945..25335703,2	K562	blood:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10456321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192665	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192812	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192951	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5009714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555189	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555190	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555191	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555192	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555193	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555194	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746360	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746606	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752550	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770388	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:25325200-25336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:25325200-25336400	Weak transcription	Lung	lung
4	chr6:25327600-25337400	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:25328200-25336800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:25328200-25338200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:25329000-25336000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:25329400-25336200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:25329400-25336400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:25329600-25336400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:25330000-25335200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:25330200-25335000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:25330400-25337200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:25330600-25335800	Weak transcription	Esophagus	oesophagus
15	chr6:25330600-25335800	Weak transcription	Gastric	stomach
16	chr6:25331000-25335800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25331000-25336000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:25331200-25335600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:25331200-25336800	Enhancers	Right Atrium	heart
20	chr6:25331400-25335000	Weak transcription	Primary T cells from cord blood	blood
21	chr6:25331400-25335400	Enhancers	Stomach Mucosa	stomach
22	chr6:25331400-25336600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:25331800-25336400	Weak transcription	Pancreas	Pancrea
24	chr6:25331800-25341800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:25332000-25336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:25332000-25336200	Weak transcription	NHEK	skin
27	chr6:25332000-25336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:25332000-25336600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:25332000-25337200	Weak transcription	Fetal Brain Female	brain
30	chr6:25332000-25337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:25332000-25337800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:25332000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:25332000-25342600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:25332000-25342600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:25332000-25346800	Weak transcription	Ovary	ovary
36	chr6:25332200-25337600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25332400-25334400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:25332400-25334400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:25332600-25334400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:25332600-25336400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:25332600-25336800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:25332600-25339800	Weak transcription	Colonic Mucosa	Colon
43	chr6:25332800-25335200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:25332800-25337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:25332800-25341200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:25333000-25334400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:25333000-25334600	Enhancers	Brain Anterior Caudate	brain
48	chr6:25333200-25334400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr6:25333200-25343800	Enhancers	Fetal Intestine Small	intestine
50	chr6:25333400-25334800	Weak transcription	Primary B cells from peripheral blood	blood

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