Variant report

Variant	rs4639
Chromosome Location	chr8:11644751-11644752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr8:11644465-11644811	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:11643528..11645314-chr8:11650082..11652912,2	MCF-7	breast:
2	chr8:11641389..11643325-chr8:11643341..11646162,4	K562	blood:
3	chr8:11644178..11646906-chr8:11648968..11651779,2	K562	blood:
4	chr8:11639903..11643106-chr8:11643341..11646162,3	K562	blood:
5	chr8:11644010..11646575-chr8:11710269..11712161,2	MCF-7	breast:

No data

Variant related genes	Relation type
SUB1P1	TF binding region
ENSG00000164733	Chromatin interaction
ENSG00000154328	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004712	0.84[CEU][hapmap]
rs1090107	0.87[AMR][1000 genomes]
rs1466785	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1534862	0.83[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2686187	0.96[CEU][hapmap]
rs2740435	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2740439	0.82[ASN][1000 genomes]
rs4840581	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs6601606	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs67631516	0.90[ASN][1000 genomes]
rs6993013	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs804258	0.96[CEU][hapmap]
rs804261	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs804263	0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs804265	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs804266	0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs804270	0.85[AMR][1000 genomes]
rs804271	0.87[EUR][1000 genomes]
rs804276	0.95[CEU][hapmap]
rs8191593	0.80[JPT][hapmap]
rs8191600	0.82[ASN][1000 genomes]
rs8191602	0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs8191609	0.81[ASN][1000 genomes]
rs8191613	0.91[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs8191614	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs8191618	0.83[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs8191631	0.85[ASN][1000 genomes]
rs8191634	0.83[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs8191636	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs8191652	0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs8191664	0.80[JPT][hapmap]
rs8191678	0.95[ASN][1000 genomes]
rs904015	0.83[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4639	NEIL2	cis	Thyroid	GTEx
rs4639	NEIL2	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11628400-11647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr8:11628400-11653000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr8:11628400-11656800	Weak transcription	Small Intestine	intestine
4	chr8:11628600-11647200	Weak transcription	Fetal Heart	heart
5	chr8:11628800-11646800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:11629600-11645800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr8:11634400-11645000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:11634600-11645200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:11635200-11644800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:11635400-11645400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:11636000-11645600	Weak transcription	Hela-S3	cervix
12	chr8:11636400-11645600	Strong transcription	Fetal Stomach	stomach
13	chr8:11636600-11645000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:11636600-11645800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr8:11636800-11659400	Weak transcription	Thymus	Thymus
16	chr8:11637600-11645600	Strong transcription	Primary B cells from cord blood	blood
17	chr8:11639000-11645400	Weak transcription	HUVEC	blood vessel
18	chr8:11640000-11645000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr8:11640200-11645600	Strong transcription	Fetal Muscle Leg	muscle
20	chr8:11640400-11644800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:11640400-11644800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr8:11640400-11645000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:11640400-11645000	Strong transcription	Brain Anterior Caudate	brain
24	chr8:11640400-11645000	Strong transcription	Brain Cingulate Gyrus	brain
25	chr8:11640400-11645600	Strong transcription	HSMMtube	muscle
26	chr8:11640600-11644800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:11640600-11644800	Strong transcription	Liver	Liver
28	chr8:11640600-11644800	Strong transcription	Brain Hippocampus Middle	brain
29	chr8:11640600-11644800	Strong transcription	HepG2	liver
30	chr8:11640600-11645800	Strong transcription	Fetal Intestine Small	intestine
31	chr8:11640800-11644800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:11640800-11645000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr8:11640800-11645000	Strong transcription	Fetal Brain Female	brain
34	chr8:11640800-11658600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:11641000-11645000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:11641000-11645000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr8:11641000-11645400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr8:11641000-11658000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:11641000-11659600	Weak transcription	Right Atrium	heart
40	chr8:11641200-11644800	Strong transcription	Primary T cells from cord blood	blood
41	chr8:11641200-11645200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr8:11641200-11658400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr8:11641200-11659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr8:11641400-11645400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr8:11641400-11645400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr8:11641400-11645400	Weak transcription	HMEC	breast
47	chr8:11641400-11645400	Weak transcription	NHDF-Ad	bronchial
48	chr8:11641400-11645600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr8:11641400-11645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:11641400-11648600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links