Variant report

Variant	rs7663321
Chromosome Location	chr4:107055190-107055191
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10003024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10008428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10016884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10018910	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10030019	0.95[CEU][hapmap];0.86[YRI][hapmap]
rs11097912	0.95[CEU][hapmap];0.86[YRI][hapmap]
rs11732251	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11732791	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11931386	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11932523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12509640	0.95[CEU][hapmap]
rs12510966	0.95[CEU][hapmap]
rs12513345	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12642691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12642900	0.86[YRI][hapmap]
rs13101612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs13114479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs13121614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13138528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17272618	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3109955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3109958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3113250	1.00[CEU][hapmap]
rs3113252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3133168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4364267	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs4374692	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4382109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4508971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4569824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4577583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4600995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6819081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6836198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6844105	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6846579	0.95[CEU][hapmap]
rs6849573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6853554	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7438546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7657962	0.95[CEU][hapmap]
rs7662592	0.95[CEU][hapmap]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7668276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7673101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7678847	0.95[CEU][hapmap];0.85[YRI][hapmap]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7692652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7693333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7693448	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv511247	chr4:107022702-107065220	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv879701	chr4:107024776-107163128	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv4450	chr4:107037823-107082669	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv508301	chr4:107049086-107092730	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv1851766	chr4:107052107-107062671	ZNF genes & repeats Strong transcription Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv437409	chr4:107052107-107064347	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv437410	chr4:107052107-107064347	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv437411	chr4:107052107-107074097	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv3467678	chr4:107054603-107060101	Strong transcription Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3467679	chr4:107054603-107060101	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7663321	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs7663321	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107032000-107058200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:107035200-107057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:107035600-107083200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:107037600-107056200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:107037600-107060600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:107037600-107061600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:107037600-107066400	Weak transcription	Fetal Kidney	kidney
8	chr4:107037800-107077400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:107038000-107055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:107038000-107056800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:107038000-107112000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:107053000-107055200	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr4:107053200-107055200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:107053400-107055200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:107053400-107056200	Strong transcription	Ovary	ovary
16	chr4:107053600-107055200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:107053600-107067600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:107053800-107058200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:107053800-107061400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:107053800-107064200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:107053800-107070000	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:107053800-107080000	Weak transcription	Right Ventricle	heart
23	chr4:107053800-107083400	Weak transcription	HSMM	muscle
24	chr4:107053800-107083800	Weak transcription	Left Ventricle	heart
25	chr4:107053800-107101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:107054000-107055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:107054000-107055400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:107054000-107055600	Weak transcription	Primary B cells from cord blood	blood
29	chr4:107054000-107055600	Weak transcription	Primary T cells from cord blood	blood
30	chr4:107054000-107055600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:107054000-107055600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:107054000-107057600	Weak transcription	Brain Substantia Nigra	brain
33	chr4:107054000-107057800	Weak transcription	Fetal Thymus	thymus
34	chr4:107054000-107057800	Weak transcription	Dnd41	blood
35	chr4:107054000-107063400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:107054000-107066400	Weak transcription	Liver	Liver
37	chr4:107054000-107067000	Weak transcription	Fetal Lung	lung
38	chr4:107054000-107067000	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:107054000-107067800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:107054000-107070000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:107054000-107070400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:107054000-107074400	Weak transcription	HepG2	liver
43	chr4:107054000-107076800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:107054000-107077000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:107054000-107077000	Weak transcription	Fetal Intestine Large	intestine
46	chr4:107054000-107077400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:107054000-107077400	Weak transcription	Aorta	Aorta
48	chr4:107054000-107077400	Weak transcription	Fetal Stomach	stomach
49	chr4:107054000-107077400	Weak transcription	Lung	lung
50	chr4:107054000-107081600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links