Variant report

Variant	rs717674
Chromosome Location	chr4:22489653-22489654
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	chr4:22488399..22490950-chr4:22493521..22495053,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10516410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1564133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16872695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16872700	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16872711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16872734	1.00[CHB][hapmap]
rs16872739	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600487	1.00[YRI][hapmap]
rs4423859	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55747913	0.82[ASN][1000 genomes]
rs55785050	0.87[ASN][1000 genomes]
rs58836068	0.82[ASN][1000 genomes]
rs61793366	1.00[ASN][1000 genomes]
rs61793367	1.00[ASN][1000 genomes]
rs61793368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61793374	0.87[ASN][1000 genomes]
rs61793403	0.87[ASN][1000 genomes]
rs61793407	0.87[ASN][1000 genomes]
rs61793409	0.82[ASN][1000 genomes]
rs7664692	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7679108	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:22462000-22493200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:22484200-22490400	Enhancers	Fetal Muscle Leg	muscle
4	chr4:22484800-22492400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:22484800-22493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:22484800-22498400	Weak transcription	Gastric	stomach
7	chr4:22485000-22490200	Enhancers	Colon Smooth Muscle	Colon
8	chr4:22485000-22492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:22485000-22506000	Weak transcription	Esophagus	oesophagus
10	chr4:22485400-22492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:22485600-22492400	Weak transcription	Liver	Liver
12	chr4:22485600-22493200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:22485600-22501400	Weak transcription	Hela-S3	cervix
14	chr4:22485600-22502000	Weak transcription	A549	lung
15	chr4:22485800-22491600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:22486400-22500600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:22486600-22492200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:22486600-22492200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:22486600-22492400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:22486800-22490200	Enhancers	Left Ventricle	heart
21	chr4:22486800-22490200	Enhancers	Psoas Muscle	Psoas
22	chr4:22486800-22492400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:22487200-22490200	Enhancers	Fetal Heart	heart
24	chr4:22487200-22490200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:22487400-22489800	Enhancers	Rectal Smooth Muscle	rectum
26	chr4:22487400-22490200	Enhancers	Right Ventricle	heart
27	chr4:22487800-22490600	Enhancers	HepG2	liver
28	chr4:22487800-22492400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:22488000-22490200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:22488000-22494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:22488200-22491400	Weak transcription	Aorta	Aorta
32	chr4:22488400-22503000	Weak transcription	Small Intestine	intestine
33	chr4:22488600-22490400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr4:22488600-22516000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:22488800-22496800	Weak transcription	HMEC	breast
36	chr4:22488800-22497800	Weak transcription	NHEK	skin
37	chr4:22488800-22503600	Weak transcription	NHLF	lung
38	chr4:22489000-22490200	Enhancers	Fetal Muscle Trunk	muscle
39	chr4:22489000-22490200	Enhancers	Right Atrium	heart
40	chr4:22489000-22490400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:22489000-22490400	Weak transcription	Fetal Intestine Large	intestine
42	chr4:22489200-22489800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:22489200-22492400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:22489200-22492400	Weak transcription	Brain Anterior Caudate	brain
45	chr4:22489200-22492400	Weak transcription	Ovary	ovary
46	chr4:22489400-22490800	Weak transcription	Fetal Intestine Small	intestine
47	chr4:22489400-22492400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:22489400-22492400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:22489400-22492400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:22489400-22492400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links