Variant report

Variant	rs16961114
Chromosome Location	chr17:18215339-18215340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18207672..18211933-chr17:18214098..18218432,6	MCF-7	breast:
2	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMCR8-2	chr17:18215218-18215965	NONHSAT146173

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11078415	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11867855	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11867895	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11868708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11869515	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11869582	0.92[CEU][hapmap]
rs11869952	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871761	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11872031	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12449313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12450760	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12451555	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451698	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12451807	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12939851	0.87[EUR][1000 genomes]
rs1563373	0.84[CEU][hapmap]
rs16961133	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16961153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1962949	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1962950	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2071242	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290502	0.93[CEU][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2290503	0.93[CEU][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290504	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290505	0.92[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2294913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364628	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35738574	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3817992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862147	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3889544	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4386179	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4450455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4500798	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4556848	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4925151	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925177	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925178	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57490980	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57697650	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59366579	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072507	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072509	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072511	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072515	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072540	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072541	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072544	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62072545	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6502641	0.86[EUR][1000 genomes]
rs7211573	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7215678	1.00[CEU][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7405677	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7498	0.93[CEU][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8080168	0.84[AMR][1000 genomes]
rs8081042	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8081155	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081343	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9901160	1.00[CHB][hapmap]
rs9901707	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9909104	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9910090	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9913139	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
4	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:18201800-18216200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr17:18202200-18216600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr17:18202400-18215400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr17:18202400-18215600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:18202400-18215600	Strong transcription	Fetal Thymus	thymus
10	chr17:18202400-18216000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:18202400-18216000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:18202400-18216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:18202400-18216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:18202400-18216400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:18202400-18216400	Strong transcription	Fetal Stomach	stomach
16	chr17:18202400-18216600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:18202400-18216600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr17:18202400-18216600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr17:18202400-18216600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr17:18202600-18215600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:18202600-18215600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:18202600-18215800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:18203200-18216800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr17:18206800-18217000	Weak transcription	Stomach Mucosa	stomach
25	chr17:18208800-18217000	Weak transcription	Right Ventricle	heart
26	chr17:18210200-18217000	Weak transcription	Psoas Muscle	Psoas
27	chr17:18210400-18215400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:18210400-18215400	Weak transcription	Fetal Brain Male	brain
29	chr17:18210600-18215400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:18210600-18215400	Weak transcription	Primary T cells from cord blood	blood
31	chr17:18210600-18215400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:18210600-18215400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr17:18210600-18215600	Weak transcription	Fetal Kidney	kidney
34	chr17:18210600-18216400	Weak transcription	Small Intestine	intestine
35	chr17:18210600-18216600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr17:18210600-18217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:18210800-18215400	Weak transcription	Pancreas	Pancrea
38	chr17:18210800-18215600	Weak transcription	Colon Smooth Muscle	Colon
39	chr17:18211200-18215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:18211200-18215400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr17:18211200-18216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:18211200-18216400	Weak transcription	Primary B cells from cord blood	blood
43	chr17:18211200-18216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr17:18211200-18217000	Weak transcription	Ovary	ovary
45	chr17:18211200-18217200	Weak transcription	Aorta	Aorta
46	chr17:18211400-18215400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr17:18211400-18215400	Weak transcription	Esophagus	oesophagus
48	chr17:18211600-18215400	Weak transcription	Gastric	stomach
49	chr17:18211800-18215400	Weak transcription	Brain Angular Gyrus	brain
50	chr17:18211800-18215600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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