Variant report

Variant	rs28675750
Chromosome Location	chr4:102182961-102182962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77668693..77669518-chr4:102182394..102183036,2	HCT-116	colon:
2	chr4:102176705..102178742-chr4:102180562..102183503,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10004830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015480	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019627	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10027301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030915	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17030959	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17030989	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28379119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421266	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28464050	1.00[EUR][1000 genomes]
rs28491829	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28534411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28542998	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28553282	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28614035	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28638143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28640942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723066	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58084948	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58598913	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58898502	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72919782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102174200-102186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:102174400-102185800	Weak transcription	HMEC	breast
3	chr4:102177800-102185000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:102178000-102186600	Weak transcription	Brain Substantia Nigra	brain
5	chr4:102178200-102183000	Weak transcription	Stomach Mucosa	stomach
6	chr4:102178200-102183800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:102179000-102186800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:102180200-102185800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:102180400-102183800	Weak transcription	Small Intestine	intestine
10	chr4:102180600-102183800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:102180600-102185400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:102180600-102185800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:102180600-102186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:102180600-102186200	Weak transcription	Pancreas	Pancrea
15	chr4:102180600-102191000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:102180600-102192400	Weak transcription	Ovary	ovary
17	chr4:102180600-102197000	Weak transcription	Left Ventricle	heart
18	chr4:102180600-102203000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:102180800-102186200	Weak transcription	Gastric	stomach
20	chr4:102181200-102183800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:102181200-102183800	Weak transcription	Psoas Muscle	Psoas
22	chr4:102181200-102183800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:102181200-102184000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:102181200-102185800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:102181200-102186600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:102181200-102186800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:102181400-102183200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:102181400-102184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:102181400-102186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:102181600-102183800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:102181600-102185000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:102181800-102183000	Weak transcription	Primary B cells from cord blood	blood
33	chr4:102181800-102184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:102181800-102185600	Weak transcription	NH-A	brain
35	chr4:102182000-102185000	Weak transcription	HUVEC	blood vessel
36	chr4:102182000-102185200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:102182200-102183800	Weak transcription	Brain Anterior Caudate	brain
38	chr4:102182200-102186000	Weak transcription	NHEK	skin
39	chr4:102182400-102183800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:102182400-102184200	Weak transcription	A549	lung
41	chr4:102182600-102183800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:102182600-102183800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:102182600-102183800	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:102182600-102183800	Weak transcription	Fetal Kidney	kidney
45	chr4:102182600-102184400	Weak transcription	Adipose Nuclei	Adipose
46	chr4:102182600-102186000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:102182600-102189800	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:102182600-102192600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:102182800-102183000	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links