Variant report

Variant	rs60423930
Chromosome Location	chr1:227422445-227422446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227422402..227423241-chr1:227624998..227625702,5	MCF-7	breast:
2	chr1:227422234..227422915-chr1:227623464..227624323,2	MCF-7	breast:
3	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:
4	chr1:227422275..227423402-chr1:227625161..227626556,7	K562	blood:
5	chr1:227100019..227100963-chr1:227422287..227422908,3	MCF-7	breast:
6	chr1:227422445..227422950-chr1:227635271..227635835,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADCK3-6	chr1:227421970-227422486	NONHSAT009917

No data

Variant related genes	Relation type
ENSG00000242757	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11804924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807511	1.00[AMR][1000 genomes]
rs11807555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808055	1.00[EUR][1000 genomes]
rs11808370	1.00[EUR][1000 genomes]
rs11808613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810417	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1355816	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35099852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4364839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57660509	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57717956	1.00[EUR][1000 genomes]
rs57895961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58077821	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59396012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59523055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60039374	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60906739	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61494318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61588040	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688385	1.00[EUR][1000 genomes]
rs6696713	1.00[EUR][1000 genomes]
rs6699740	1.00[EUR][1000 genomes]
rs73086744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088692	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090609	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090689	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092512	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73096314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098345	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098350	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102326	1.00[EUR][1000 genomes]
rs73102327	1.00[EUR][1000 genomes]
rs73102341	1.00[EUR][1000 genomes]
rs73102913	1.00[AMR][1000 genomes]
rs73102948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411165	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74143320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227414200-227423400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:227414200-227453800	Weak transcription	HSMM	muscle
16	chr1:227414400-227423000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:227414400-227423000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:227415600-227422800	Weak transcription	HUVEC	blood vessel
23	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
26	chr1:227421800-227423000	Enhancers	Left Ventricle	heart
27	chr1:227422000-227422600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:227422000-227430800	Weak transcription	Ovary	ovary
29	chr1:227422200-227423600	Enhancers	Brain Anterior Caudate	brain
30	chr1:227422200-227423600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:227422200-227423800	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:227422200-227424000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:227422400-227422600	Enhancers	Brain Angular Gyrus	brain
34	chr1:227422400-227422600	Enhancers	Gastric	stomach
35	chr1:227422400-227423000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:227422400-227424000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links