Variant report

Variant	rs12673012
Chromosome Location	chr7:6486677-6486678
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6485398..6489202-chr7:6520855..6525273,5	MCF-7	breast:
2	chr7:6486176..6487864-chr7:6615659..6618201,2	MCF-7	breast:
3	chr7:6412857..6414877-chr7:6485942..6488132,2	MCF-7	breast:
4	chr7:6486201..6489628-chr7:6522463..6525039,4	MCF-7	breast:
5	chr7:6474092..6477009-chr7:6483600..6487126,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRID2IP-4	chr7:6486625-6486971	expReg_chr7_744_-

Variant related genes	Relation type
ENSG00000136247	Chromatin interaction
ENSG00000136238	Chromatin interaction
ENSG00000269781	Chromatin interaction
ENSG00000136240	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12666600	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670104	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12670121	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12673652	0.81[ASN][1000 genomes]
rs13237786	0.94[ASN][1000 genomes]
rs2272154	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2272156	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2288152	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs5020305	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55695740	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61211132	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6463557	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6944712	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6945053	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6945450	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72583273	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72583274	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7797088	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv971152	chr7:6485642-6509340	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6453000-6486800	Weak transcription	Small Intestine	intestine
2	chr7:6456800-6486800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:6485800-6486800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:6485800-6486800	Weak transcription	Gastric	stomach
5	chr7:6486200-6486800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:6486200-6486800	Flanking Active TSS	Fetal Brain Female	brain
7	chr7:6486200-6487000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr7:6486200-6487000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:6486200-6487000	Flanking Active TSS	Dnd41	blood
10	chr7:6486200-6487200	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr7:6486200-6487200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr7:6486200-6487200	Active TSS	Brain Germinal Matrix	brain
13	chr7:6486200-6487400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:6486200-6488200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:6486200-6488400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr7:6486200-6488400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr7:6486200-6488400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr7:6486200-6488400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:6486200-6488400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:6486200-6488800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr7:6486200-6489200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:6486400-6486800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:6486400-6486800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:6486400-6486800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:6486400-6486800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:6486400-6486800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr7:6486400-6486800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:6486400-6486800	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr7:6486400-6486800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr7:6486400-6486800	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr7:6486400-6486800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr7:6486400-6486800	Flanking Active TSS	Fetal Stomach	stomach
33	chr7:6486400-6486800	Flanking Active TSS	Right Ventricle	heart
34	chr7:6486400-6486800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr7:6486400-6486800	Enhancers	Spleen	Spleen
36	chr7:6486400-6486800	Flanking Active TSS	GM12878-XiMat	blood
37	chr7:6486400-6486800	Flanking Active TSS	Hela-S3	cervix
38	chr7:6486400-6486800	Flanking Active TSS	HepG2	liver
39	chr7:6486400-6487000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:6486400-6487000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr7:6486400-6487000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr7:6486400-6487000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:6486400-6487000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr7:6486400-6487000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr7:6486400-6487000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr7:6486400-6487000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr7:6486400-6487000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:6486400-6487000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:6486400-6487000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr7:6486400-6487000	Flanking Active TSS	Brain Anterior Caudate	brain

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