Variant report

Variant	rs28416479
Chromosome Location	chr4:8049526-8049527
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8048107..8050691-chr4:8051962..8053661,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10020078	1.00[ASN][1000 genomes]
rs10020169	1.00[ASN][1000 genomes]
rs16841640	1.00[ASN][1000 genomes]
rs28535319	1.00[ASN][1000 genomes]
rs4696741	1.00[ASN][1000 genomes]
rs55932143	1.00[ASN][1000 genomes]
rs56192722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57007308	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57147516	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58061467	1.00[ASN][1000 genomes]
rs58454418	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58733360	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59070213	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59525928	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60624370	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074033	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73074034	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074035	1.00[ASN][1000 genomes]
rs73074036	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074038	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074039	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	18 gene(s)	inside rSNPs	diseases
3	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong 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	13 gene(s)	inside rSNPs	diseases
5	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv470009	chr4:8015421-8085174	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv878581	chr4:8021592-8100272	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv878583	chr4:8023484-8049713	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv878584	chr4:8023484-8075134	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv878585	chr4:8023484-8116202	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv878586	chr4:8023484-8148159	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv878587	chr4:8031471-8075134	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv878588	chr4:8034772-8070793	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv878589	chr4:8034772-8089598	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv878590	chr4:8047973-8075134	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8010600-8052000	Weak transcription	Left Ventricle	heart
2	chr4:8031200-8052000	Weak transcription	Psoas Muscle	Psoas
3	chr4:8038000-8052000	Weak transcription	Right Ventricle	heart
4	chr4:8039200-8057000	Weak transcription	Gastric	stomach
5	chr4:8039400-8052400	Weak transcription	Pancreas	Pancrea
6	chr4:8039400-8056600	Weak transcription	Aorta	Aorta
7	chr4:8041200-8052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:8041800-8049600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:8041800-8052000	Weak transcription	Adipose Nuclei	Adipose
10	chr4:8043200-8049800	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:8045600-8052000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:8046000-8050800	Weak transcription	Esophagus	oesophagus
13	chr4:8046600-8052000	Weak transcription	Lung	lung
14	chr4:8046800-8051000	Weak transcription	Fetal Lung	lung
15	chr4:8047000-8050000	Weak transcription	Brain Angular Gyrus	brain
16	chr4:8047000-8050000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:8047000-8052000	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:8047000-8052000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:8047800-8049600	Bivalent Enhancer	HepG2	liver
20	chr4:8047800-8052000	Weak transcription	Colonic Mucosa	Colon
21	chr4:8047800-8052200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:8047800-8052200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:8047800-8054800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:8048200-8052000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:8048600-8052000	Weak transcription	Brain Germinal Matrix	brain
26	chr4:8048600-8054800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr4:8048800-8051200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:8049000-8053400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:8049200-8049800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr4:8049200-8050400	Enhancers	Brain Anterior Caudate	brain
31	chr4:8049200-8052000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr4:8049200-8054200	Enhancers	H9 Cell Line	embryonic stem cell
33	chr4:8049400-8049600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr4:8049400-8050400	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr4:8049400-8051600	Weak transcription	Spleen	Spleen
36	chr4:8049400-8052800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr4:8049400-8054000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links