Variant report

Variant	rs16835782
Chromosome Location	chr1:150265360-150265361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:150265304-150267140	MCF-7	breast:	n/a	chr1:150266265-150266272
2	HCFC1	chr1:150265340-150267216	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150264700..150268461-chr1:150290358..150296338,12	MCF-7	breast:
2	chr1:150263378..150268409-chr1:150334980..150339088,9	MCF-7	breast:
3	chr1:150264985..150267116-chr1:150337062..150338980,2	MCF-7	breast:
4	chr1:150240223..150242953-chr1:150263372..150266971,3	K562	blood:
5	chr1:150264496..150269056-chr1:150292330..150296241,7	MCF-7	breast:
6	chr1:150206794..150209349-chr1:150261451..150266044,4	K562	blood:
7	chr1:150240546..150242221-chr1:150264940..150266566,2	K562	blood:
8	chr1:150234315..150237513-chr1:150265191..150267090,3	K562	blood:
9	chr1:150264617..150266703-chr1:150314248..150316568,2	MCF-7	breast:
10	chr1:149855825..149859735-chr1:150264985..150268023,4	MCF-7	breast:
11	chr1:150264361..150267747-chr1:150292578..150295568,3	K562	blood:
12	chr1:150265074..150268122-chr1:150334427..150338986,4	K562	blood:
13	chr1:150205825..150209635-chr1:150259375..150267858,10	K562	blood:
14	chr1:150265031..150267516-chr1:150292699..150295000,3	K562	blood:
15	chr1:150206170..150208675-chr1:150264452..150269195,6	MCF-7	breast:

No data

Variant related genes	Relation type
MRPS21	TF binding region
ENSG00000163125	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000118298	Chromatin interaction
ENSG00000184260	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10788873	0.83[YRI][hapmap]
rs12116970	0.81[ASN][1000 genomes]
rs12718416	0.81[ASN][1000 genomes]
rs12729719	0.81[ASN][1000 genomes]
rs13057	0.82[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16830437	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16835699	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16835708	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16835791	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16835911	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16836130	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16836139	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16836442	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16836576	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16836594	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16836601	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16836786	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16836940	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs16836943	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2015966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2275245	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2275778	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2275779	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3737319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3738322	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3806389	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs3850843	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4926420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4926421	0.83[JPT][hapmap]
rs4926430	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4970925	0.85[ASN][1000 genomes]
rs4970927	0.81[ASN][1000 genomes]
rs4970946	0.81[ASN][1000 genomes]
rs4970947	0.85[ASN][1000 genomes]
rs522068	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56882505	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56909494	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57163995	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57272513	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57361164	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57971032	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58373639	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58419446	0.85[ASN][1000 genomes]
rs58516261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59367061	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59378360	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59639798	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59662772	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60456922	0.85[ASN][1000 genomes]
rs60459288	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60531845	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60730811	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60758881	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61605510	0.84[AMR][1000 genomes]
rs6679726	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6680391	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6700009	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6700607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs71622690	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73011380	0.91[ASN][1000 genomes]
rs73011384	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73011400	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73013119	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73013129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73015063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73015078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73015081	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73015095	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73015096	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73017006	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73017073	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73017086	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73017092	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73017102	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019017	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019018	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019020	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019021	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019027	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73019028	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7543314	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs871527	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs953127	0.84[AMR][1000 genomes];0.85[ASN][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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150254600-150266200	Weak transcription	Small Intestine	intestine
2	chr1:150255400-150265400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:150255400-150265800	Weak transcription	HSMMtube	muscle
4	chr1:150255400-150266200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:150255600-150265800	Weak transcription	Aorta	Aorta
6	chr1:150255800-150265400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:150255800-150266000	Weak transcription	Gastric	stomach
8	chr1:150256000-150265400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:150256000-150265400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:150256000-150265400	Weak transcription	Fetal Lung	lung
11	chr1:150256000-150265400	Weak transcription	Psoas Muscle	Psoas
12	chr1:150256000-150265400	Weak transcription	Right Ventricle	heart
13	chr1:150256000-150265400	Weak transcription	NHEK	skin
14	chr1:150256000-150265600	Weak transcription	NH-A	brain
15	chr1:150256000-150265800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:150256000-150265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:150256000-150266000	Weak transcription	Pancreas	Pancrea
18	chr1:150256200-150265400	Weak transcription	Brain Germinal Matrix	brain
19	chr1:150256200-150265400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:150256200-150265400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:150256200-150265600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:150256200-150265600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:150256200-150265800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:150256200-150265800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:150256200-150265800	Weak transcription	HMEC	breast
26	chr1:150256200-150266000	Weak transcription	Lung	lung
27	chr1:150256200-150266000	Weak transcription	Spleen	Spleen
28	chr1:150256400-150265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:150256400-150265600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:150257000-150265400	Weak transcription	Fetal Heart	heart
31	chr1:150257200-150265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:150257400-150265600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:150257600-150265600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:150258400-150266000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:150259200-150265400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:150259400-150265400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:150259400-150265400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:150259400-150265400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:150259400-150265400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:150259400-150265400	Weak transcription	Brain Substantia Nigra	brain
41	chr1:150259400-150265400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:150259400-150265400	Weak transcription	Fetal Stomach	stomach
43	chr1:150259400-150265400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:150259400-150265600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:150259400-150265600	Weak transcription	NHDF-Ad	bronchial
46	chr1:150259400-150265800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:150259400-150265800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:150259400-150265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:150259400-150265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:150259400-150266000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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