Variant report

Variant	rs35270682
Chromosome Location	chr17:37727668-37727669
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37720810..37722630-chr17:37726037..37729027,2	MCF-7	breast:
2	chr17:37724265..37726449-chr17:37726824..37730353,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK12-1	chr17:37727663-37728388	NONHSAT053446

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12943456	0.82[AFR][1000 genomes]
rs12944298	0.90[AFR][1000 genomes]
rs12950784	0.84[AFR][1000 genomes]
rs34079604	0.88[AFR][1000 genomes]
rs34207136	0.81[AFR][1000 genomes]
rs34458385	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34518049	0.81[AFR][1000 genomes]
rs35442489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35598597	0.82[AFR][1000 genomes]
rs35701477	0.81[AFR][1000 genomes]
rs35929798	0.81[AFR][1000 genomes]
rs35986399	0.81[AFR][1000 genomes]
rs36025330	0.90[AFR][1000 genomes]
rs36172452	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887260	0.81[EUR][1000 genomes]
rs4988981	0.88[AFR][1000 genomes]
rs55976670	0.87[ASN][1000 genomes]
rs56277614	0.81[EUR][1000 genomes]
rs56301513	0.82[EUR][1000 genomes]
rs57009492	0.87[ASN][1000 genomes]
rs57059040	0.94[AFR][1000 genomes]
rs58452873	0.87[AFR][1000 genomes]
rs60403655	0.87[ASN][1000 genomes]
rs67466585	0.87[ASN][1000 genomes]
rs67966109	0.87[ASN][1000 genomes]
rs71369773	0.82[AFR][1000 genomes]
rs71369774	0.91[AFR][1000 genomes]
rs71369775	0.93[AFR][1000 genomes]
rs7219611	0.84[AFR][1000 genomes]
rs7219683	0.91[AFR][1000 genomes]
rs7224847	0.93[AFR][1000 genomes]
rs72827114	0.93[EUR][1000 genomes]
rs72827126	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72827138	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827139	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827140	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827159	0.82[EUR][1000 genomes]
rs72827162	0.81[EUR][1000 genomes]
rs8081144	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
2	chr17:37701000-37728800	Strong transcription	Liver	Liver
3	chr17:37708800-37729400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:37710400-37729400	Weak transcription	HMEC	breast
5	chr17:37710400-37729600	Weak transcription	NHEK	skin
6	chr17:37710800-37730400	Weak transcription	Stomach Mucosa	stomach
7	chr17:37713000-37729200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:37713200-37729600	Weak transcription	NHDF-Ad	bronchial
9	chr17:37714000-37729600	Weak transcription	NHLF	lung
10	chr17:37714600-37728600	Weak transcription	Brain Angular Gyrus	brain
11	chr17:37714600-37729600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:37716200-37727800	Strong transcription	Primary T cells from cord blood	blood
13	chr17:37719600-37729600	Weak transcription	HUVEC	blood vessel
14	chr17:37720000-37729600	Weak transcription	NH-A	brain
15	chr17:37720200-37727800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr17:37720400-37729200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr17:37720400-37729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:37720400-37730200	Enhancers	Fetal Brain Male	brain
19	chr17:37720600-37729600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:37720600-37729600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:37720800-37729000	Weak transcription	Hela-S3	cervix
22	chr17:37720800-37729200	Weak transcription	Right Atrium	heart
23	chr17:37721000-37729600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:37721000-37729600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:37721200-37728800	Strong transcription	Fetal Stomach	stomach
26	chr17:37721400-37727800	Genic enhancers	Fetal Muscle Leg	muscle
27	chr17:37721400-37728200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:37721400-37729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:37721400-37729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:37721400-37729600	Weak transcription	Psoas Muscle	Psoas
31	chr17:37721400-37736200	Weak transcription	Fetal Heart	heart
32	chr17:37722400-37727800	Strong transcription	Primary B cells from cord blood	blood
33	chr17:37722400-37728000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:37723200-37728800	Strong transcription	A549	lung
35	chr17:37723400-37729600	Weak transcription	Colon Smooth Muscle	Colon
36	chr17:37723800-37730200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr17:37724000-37729600	Weak transcription	Fetal Kidney	kidney
38	chr17:37724800-37729600	Weak transcription	Brain Hippocampus Middle	brain
39	chr17:37724800-37729600	Weak transcription	Left Ventricle	heart
40	chr17:37724800-37729600	Weak transcription	Osteobl	bone
41	chr17:37725000-37729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:37725600-37728400	Enhancers	Fetal Brain Female	brain
43	chr17:37725600-37729600	Weak transcription	Ovary	ovary
44	chr17:37725800-37728600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr17:37725800-37728600	Weak transcription	Pancreas	Pancrea
46	chr17:37725800-37728600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr17:37725800-37728800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:37725800-37729200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr17:37725800-37729200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:37725800-37729600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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