Variant report

Variant	rs59768249
Chromosome Location	chr1:46470174-46470175
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	chr1:46467498..46470215-chr1:46486949..46488855,2	K562	blood:
2	chr1:46466152..46468526-chr1:46469622..46471885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086015	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17102066	1.00[AMR][1000 genomes]
rs2275425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28363193	1.00[AMR][1000 genomes]
rs41378047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4297232	1.00[AMR][1000 genomes]
rs57121950	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57402001	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57959845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57991520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58888694	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59669845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59919818	1.00[AMR][1000 genomes]
rs59974520	1.00[AMR][1000 genomes]
rs60789947	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60933200	1.00[AMR][1000 genomes]
rs61169182	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61178863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	nsv546158	chr1:46216575-46495434	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv870911	chr1:46216575-46498375	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	nsv431268	chr1:46223080-46495480	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv1007759	chr1:46248667-46493959	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv534945	chr1:46248667-46493959	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv916232	chr1:46248686-46493918	Genic enhancers Active TSS Flanking Active TSS Enhancers Weak transcription 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	16 gene(s)	inside rSNPs	diseases
14	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv546161	chr1:46311275-46498375	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
18	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
19	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
20	nsv829737	chr1:46352900-46506424	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
22	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
23	nsv522438	chr1:46462881-46500993	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
24	esv1795204	chr1:46466373-46504466	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
25	esv1829371	chr1:46466373-46504466	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46438200-46471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:46445600-46472000	Weak transcription	A549	lung
3	chr1:46445600-46475600	Weak transcription	Stomach Mucosa	stomach
4	chr1:46448400-46472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:46448800-46470400	Weak transcription	Fetal Lung	lung
6	chr1:46453600-46472000	Weak transcription	Primary T cells from cord blood	blood
7	chr1:46455000-46471600	Weak transcription	Lung	lung
8	chr1:46455400-46471200	Weak transcription	Aorta	Aorta
9	chr1:46457000-46472800	Weak transcription	Small Intestine	intestine
10	chr1:46458600-46471400	Weak transcription	Primary B cells from cord blood	blood
11	chr1:46459800-46471000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:46460400-46471800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:46461000-46474000	Weak transcription	NH-A	brain
14	chr1:46461400-46488000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:46461600-46471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:46461800-46471800	Weak transcription	Ovary	ovary
17	chr1:46461800-46474000	Weak transcription	Thymus	Thymus
18	chr1:46462000-46472000	Weak transcription	HUVEC	blood vessel
19	chr1:46462200-46471800	Weak transcription	NHDF-Ad	bronchial
20	chr1:46462400-46471400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:46463000-46471200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:46463000-46473000	Weak transcription	GM12878-XiMat	blood
23	chr1:46463200-46471800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:46463200-46473200	Weak transcription	Right Atrium	heart
25	chr1:46463600-46471400	Weak transcription	Osteobl	bone
26	chr1:46463600-46471800	Weak transcription	Adipose Nuclei	Adipose
27	chr1:46463600-46471800	Weak transcription	Gastric	stomach
28	chr1:46463800-46471600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:46463800-46473600	Weak transcription	NHEK	skin
30	chr1:46464000-46472000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:46464000-46472800	Weak transcription	Psoas Muscle	Psoas
32	chr1:46464200-46471800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:46464200-46472800	Weak transcription	Brain Substantia Nigra	brain
34	chr1:46464200-46472800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:46464200-46474000	Weak transcription	Fetal Thymus	thymus
36	chr1:46464200-46474600	Weak transcription	Fetal Brain Male	brain
37	chr1:46464600-46471400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:46464600-46475000	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:46464600-46478800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:46464600-46479200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:46464800-46471800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:46464800-46472400	Weak transcription	Pancreas	Pancrea
43	chr1:46464800-46474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:46464800-46474000	Weak transcription	Spleen	Spleen
45	chr1:46464800-46479400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:46465000-46479200	Strong transcription	Fetal Stomach	stomach
47	chr1:46465200-46471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:46465200-46471600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:46465200-46472000	Weak transcription	Hela-S3	cervix
50	chr1:46465200-46476000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links