Variant report

Variant	rs6717889
Chromosome Location	chr2:96193576-96193577
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	YY1	chr2:96193392-96193587	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96192581..96194179-chr2:96218990..96220757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272913	TF binding region
ENSG00000229689	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs6740380	0.86[AFR][1000 genomes]
rs72948011	0.90[AFR][1000 genomes]
rs72948013	0.85[AFR][1000 genomes]
rs72948022	0.90[AFR][1000 genomes]
rs72948023	0.90[AFR][1000 genomes]
rs72948026	1.00[AFR][1000 genomes]
rs72948035	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv834300	chr2:96087967-96337557	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv1006283	chr2:96159804-96206863	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001305	chr2:96161688-96259200	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1008062	chr2:96166970-96259200	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv998984	chr2:96166970-96290275	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv998587	chr2:96170558-96378228	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv961451	chr2:96176161-96194972	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96191200-96193600	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:96191200-96193600	Active TSS	HSMM	muscle
3	chr2:96191200-96193800	Active TSS	Fetal Kidney	kidney
4	chr2:96191400-96193600	Active TSS	Brain Angular Gyrus	brain
5	chr2:96191400-96193600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:96191400-96193800	Active TSS	Primary T cells from cord blood	blood
7	chr2:96191400-96194200	Active TSS	GM12878-XiMat	blood
8	chr2:96191600-96193600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:96191600-96193600	Active TSS	Brain Anterior Caudate	brain
10	chr2:96191600-96193600	Active TSS	Brain Germinal Matrix	brain
11	chr2:96191600-96193600	Active TSS	Fetal Brain Female	brain
12	chr2:96191600-96193600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:96191600-96194600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:96191800-96193600	Active TSS	Psoas Muscle	Psoas
15	chr2:96191800-96193800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:96191800-96193800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:96191800-96194000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:96192000-96193600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:96192000-96193600	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr2:96192000-96193600	Active TSS	Stomach Smooth Muscle	stomach
21	chr2:96192000-96193600	Active TSS	NHEK	skin
22	chr2:96192000-96194000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:96192200-96193600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:96192200-96193600	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr2:96192200-96193600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:96192200-96193600	Active TSS	Duodenum Mucosa	Duodenum
27	chr2:96192200-96193800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:96192200-96193800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr2:96192200-96194200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:96192200-96197800	Weak transcription	Fetal Heart	heart
31	chr2:96192400-96196800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:96192600-96194200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:96193000-96194000	Active TSS	HMEC	breast
34	chr2:96193000-96196400	Weak transcription	Spleen	Spleen
35	chr2:96193200-96193600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr2:96193200-96193600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:96193200-96193600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:96193200-96193600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:96193200-96193600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr2:96193200-96193600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:96193200-96193600	Active TSS	Adipose Nuclei	Adipose
42	chr2:96193200-96193600	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:96193200-96193600	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:96193200-96193600	Enhancers	Fetal Muscle Trunk	muscle
45	chr2:96193200-96193600	Active TSS	HUVEC	blood vessel
46	chr2:96193200-96193600	Active TSS	NH-A	brain
47	chr2:96193200-96193800	Enhancers	Primary B cells from peripheral blood	blood
48	chr2:96193200-96193800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:96193200-96193800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:96193200-96193800	Enhancers	Stomach Mucosa	stomach

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