Variant report

Variant	rs2690124
Chromosome Location	chr6:25305147-25305148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25304384..25306204-chr6:25317255..25319611,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1046141	1.00[CHD][hapmap]
rs11759648	1.00[CHD][hapmap]
rs1880271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900552	1.00[CHD][hapmap]
rs2044553	1.00[CHD][hapmap]
rs2690047	1.00[CHD][hapmap]
rs2690076	1.00[CHD][hapmap]
rs2690102	1.00[CHD][hapmap]
rs2690116	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2690119	0.87[AFR][1000 genomes]
rs2690122	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2744282	1.00[CHD][hapmap]
rs2744292	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs2744295	0.91[AFR][1000 genomes]
rs6456653	1.00[CHD][hapmap]
rs7739830	1.00[CHD][hapmap]
rs7755584	1.00[CHD][hapmap]
rs940405	1.00[CHD][hapmap]
rs9467496	1.00[CHD][hapmap]

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	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25294200-25311200	Weak transcription	Lung	lung
3	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:25301200-25305400	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:25301600-25311600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:25301800-25305600	Enhancers	Fetal Intestine Large	intestine
8	chr6:25301800-25306000	Enhancers	Fetal Intestine Small	intestine
9	chr6:25302000-25312800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:25302600-25311200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:25302600-25312400	Weak transcription	Thymus	Thymus
12	chr6:25302800-25307600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:25302800-25312200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:25303200-25306400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:25303200-25308200	Weak transcription	Ovary	ovary
16	chr6:25303200-25311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:25303200-25311600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:25303400-25305400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:25303400-25306400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:25303400-25306600	Weak transcription	Aorta	Aorta
22	chr6:25303400-25306800	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:25303400-25310200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:25303400-25311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
26	chr6:25303800-25305600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:25303800-25306000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25303800-25308000	Weak transcription	Fetal Heart	heart
29	chr6:25303800-25308000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:25303800-25308000	Weak transcription	HSMMtube	muscle
31	chr6:25303800-25311800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:25303800-25312400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:25304000-25305800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:25304000-25305800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr6:25304000-25307400	Weak transcription	Stomach Mucosa	stomach
36	chr6:25304000-25308200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:25304000-25311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:25304000-25311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:25304200-25305600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr6:25304200-25305800	Enhancers	Small Intestine	intestine
41	chr6:25304200-25309400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:25304200-25310200	Weak transcription	NHLF	lung
43	chr6:25304200-25311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:25304600-25305400	Weak transcription	Colonic Mucosa	Colon
45	chr6:25304800-25305200	Enhancers	Liver	Liver
46	chr6:25304800-25305600	Enhancers	Primary hematopoietic stem cells	blood
47	chr6:25304800-25305600	Enhancers	Fetal Lung	lung
48	chr6:25305000-25305400	Active TSS	Fetal Brain Male	brain
49	chr6:25305000-25306000	Enhancers	A549	lung
50	chr6:25305000-25310400	Weak transcription	Right Atrium	heart

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