Variant report

Variant	rs17413344
Chromosome Location	chr18:9120061-9120062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:9119994-9120097	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9102444..9104093-chr18:9117938..9120762,2	MCF-7	breast:
2	chr18:9117343..9120126-chr18:9132921..9134783,2	K562	blood:
3	chr18:9118013..9119695-chr18:9119782..9122411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263847	TF binding region
ENSG00000266053	Chromatin interaction
ENSG00000178127	Chromatin interaction
ENSG00000265257	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10164138	1.00[YRI][hapmap]
rs1046483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10502391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11659948	1.00[JPT][hapmap]
rs12326829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13381849	0.87[YRI][hapmap]
rs1443597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1443598	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16954886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs16954905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs16954914	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17497377	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17498752	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.80[EUR][1000 genomes]
rs17498969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs17499116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1899668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2120316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2298548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2377962	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28520663	0.80[EUR][1000 genomes]
rs28578690	0.81[ASN][1000 genomes]
rs28619483	0.80[EUR][1000 genomes]
rs2864515	0.80[EUR][1000 genomes]
rs2864527	1.00[YRI][hapmap]
rs3213925	0.80[EUR][1000 genomes]
rs3744822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3744823	0.80[EUR][1000 genomes]
rs4356535	0.80[EUR][1000 genomes]
rs4449017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4490062	0.80[EUR][1000 genomes]
rs5011606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs56996721	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs57716132	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58350342	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs59018067	0.80[EUR][1000 genomes]
rs59616258	0.80[EUR][1000 genomes]
rs59633812	0.80[EUR][1000 genomes]
rs59983698	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60119987	0.80[EUR][1000 genomes]
rs60143204	0.84[EUR][1000 genomes]
rs60354371	0.80[EUR][1000 genomes]
rs7229105	0.84[EUR][1000 genomes]
rs7235358	0.80[EUR][1000 genomes]
rs7242002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72935229	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72935233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935248	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935253	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72935258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72935260	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935263	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935265	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935266	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935267	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935274	0.87[EUR][1000 genomes]
rs72937244	0.84[EUR][1000 genomes]
rs72937245	0.84[EUR][1000 genomes]
rs72937248	0.84[EUR][1000 genomes]
rs72937250	0.84[EUR][1000 genomes]
rs72937257	0.81[EUR][1000 genomes]
rs72937258	0.80[EUR][1000 genomes]
rs72937259	0.80[EUR][1000 genomes]
rs72937263	0.80[EUR][1000 genomes]
rs72937267	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs72937270	0.80[EUR][1000 genomes]
rs72937287	0.80[EUR][1000 genomes]
rs72937291	0.80[EUR][1000 genomes]
rs72937297	0.80[EUR][1000 genomes]
rs72937301	0.80[EUR][1000 genomes]
rs72939207	0.80[EUR][1000 genomes]
rs72939211	0.80[EUR][1000 genomes]
rs72939216	0.84[AFR][1000 genomes]
rs72939219	0.80[EUR][1000 genomes]
rs72939220	0.80[EUR][1000 genomes]
rs72939221	0.80[EUR][1000 genomes]
rs72939224	0.80[EUR][1000 genomes]
rs72939227	0.80[EUR][1000 genomes]
rs72939230	0.80[EUR][1000 genomes]
rs72939231	0.80[EUR][1000 genomes]
rs72939232	0.80[EUR][1000 genomes]
rs72939235	0.80[EUR][1000 genomes]
rs72939239	0.80[EUR][1000 genomes]
rs7505002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7506375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7506561	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8094979	0.87[EUR][1000 genomes]
rs8096630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8098544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs8099583	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9652921	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9675513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9748485	0.80[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	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9104400-9130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9106200-9123200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:9107000-9135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9107400-9135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:9107600-9123200	Weak transcription	Thymus	Thymus
6	chr18:9107800-9134600	Weak transcription	Fetal Brain Male	brain
7	chr18:9108200-9123000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:9108200-9127200	Weak transcription	Fetal Brain Female	brain
9	chr18:9109600-9123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:9111200-9125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr18:9111600-9126800	Weak transcription	Colonic Mucosa	Colon
12	chr18:9111800-9123400	Weak transcription	Fetal Stomach	stomach
13	chr18:9114000-9121000	Weak transcription	Fetal Muscle Leg	muscle
14	chr18:9114000-9123200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr18:9114000-9123400	Weak transcription	Fetal Intestine Small	intestine
16	chr18:9114000-9127400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:9114000-9130800	Weak transcription	Ovary	ovary
18	chr18:9115400-9134600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:9115800-9134800	Strong transcription	Dnd41	blood
20	chr18:9116600-9120400	Enhancers	Brain Substantia Nigra	brain
21	chr18:9116800-9135200	Strong transcription	Fetal Thymus	thymus
22	chr18:9117200-9134800	Weak transcription	Brain Germinal Matrix	brain
23	chr18:9117400-9123400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr18:9117400-9125800	Weak transcription	Right Atrium	heart
25	chr18:9117400-9132000	Strong transcription	Fetal Intestine Large	intestine
26	chr18:9117400-9135200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr18:9117400-9135600	Weak transcription	Esophagus	oesophagus
28	chr18:9117400-9135800	Weak transcription	Gastric	stomach
29	chr18:9117600-9123400	Weak transcription	Left Ventricle	heart
30	chr18:9117600-9123400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr18:9117600-9127400	Weak transcription	Spleen	Spleen
32	chr18:9117600-9134800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr18:9117600-9135200	Weak transcription	Psoas Muscle	Psoas
34	chr18:9117600-9135800	Weak transcription	Pancreas	Pancrea
35	chr18:9117800-9120200	Enhancers	HSMMtube	muscle
36	chr18:9117800-9122400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr18:9117800-9124000	Strong transcription	HepG2	liver
38	chr18:9117800-9127200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr18:9117800-9128800	Weak transcription	Lung	lung
40	chr18:9117800-9132600	Weak transcription	Aorta	Aorta
41	chr18:9117800-9135000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr18:9117800-9135600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:9117800-9135800	Weak transcription	Small Intestine	intestine
44	chr18:9118200-9121400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
45	chr18:9118200-9124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr18:9118200-9134400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:9118200-9135000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr18:9118400-9120400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr18:9118400-9121400	Genic enhancers	Liver	Liver
50	chr18:9118400-9134400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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