Variant report

Variant	rs3857756
Chromosome Location	chr7:5800769-5800770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5798985..5801479-chr7:5819651..5822590,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSPH10B-2	chr7:5800719-5800769	NONHSAT118935

Variant related genes	Relation type
ENSG00000011275	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10807950	0.88[ASN][1000 genomes]
rs10951961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11763027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1640234	1.00[JPT][hapmap]
rs1725186	0.82[ASN][1000 genomes]
rs1725187	0.82[ASN][1000 genomes]
rs1990835	0.88[ASN][1000 genomes]
rs2008425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2112008	0.88[ASN][1000 genomes]
rs2161012	0.88[ASN][1000 genomes]
rs2287595	0.80[YRI][hapmap]
rs2345863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2345864	0.88[ASN][1000 genomes]
rs2908430	0.82[ASN][1000 genomes]
rs3735288	0.82[ASN][1000 genomes]
rs4720636	0.88[ASN][1000 genomes]
rs4720639	0.88[ASN][1000 genomes]
rs4720643	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4724714	0.88[ASN][1000 genomes]
rs4724716	0.88[ASN][1000 genomes]
rs4724720	0.88[ASN][1000 genomes]
rs4724721	0.88[ASN][1000 genomes]
rs4724723	0.88[ASN][1000 genomes]
rs4724727	1.00[CEU][hapmap]
rs6463508	0.88[ASN][1000 genomes]
rs6463515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6947405	0.88[ASN][1000 genomes]
rs6956990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6969486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs710939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs710940	0.82[ASN][1000 genomes]
rs710942	0.82[ASN][1000 genomes]
rs7784394	0.88[ASN][1000 genomes]
rs7790499	0.88[ASN][1000 genomes]
rs7794571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs852261	0.88[ASN][1000 genomes]
rs852262	0.88[ASN][1000 genomes]
rs852264	0.88[ASN][1000 genomes]
rs852378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852393	0.88[ASN][1000 genomes]
rs852395	0.88[ASN][1000 genomes]
rs852398	0.88[ASN][1000 genomes]
rs852399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs852401	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs852404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs852405	0.88[ASN][1000 genomes]
rs852407	0.82[ASN][1000 genomes]
rs852408	0.88[ASN][1000 genomes]
rs852411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs852412	0.82[ASN][1000 genomes]
rs852413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs852414	0.88[ASN][1000 genomes]
rs852416	0.82[ASN][1000 genomes]
rs852418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs852437	0.82[ASN][1000 genomes]
rs852438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852440	0.82[ASN][1000 genomes]
rs852442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852449	0.88[ASN][1000 genomes]
rs852451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852455	0.82[ASN][1000 genomes]
rs852458	0.82[ASN][1000 genomes]
rs852459	0.82[ASN][1000 genomes]
rs852460	0.82[ASN][1000 genomes]
rs852462	0.82[ASN][1000 genomes]
rs852465	0.82[ASN][1000 genomes]
rs852466	0.82[ASN][1000 genomes]
rs852467	0.82[ASN][1000 genomes]
rs852469	0.82[ASN][1000 genomes]
rs852471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852474	0.88[ASN][1000 genomes]
rs852475	0.82[ASN][1000 genomes]
rs852476	0.82[ASN][1000 genomes]
rs852477	0.82[ASN][1000 genomes]
rs852486	1.00[CEU][hapmap]
rs852487	0.82[ASN][1000 genomes]
rs852490	0.82[ASN][1000 genomes]
rs852514	0.82[ASN][1000 genomes]
rs852518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852521	0.82[ASN][1000 genomes]
rs852523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs852524	0.82[ASN][1000 genomes]
rs852525	0.82[ASN][1000 genomes]
rs941016	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
3	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
4	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription 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 miRNA target site	336 gene(s)	inside rSNPs	diseases
5	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
6	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
7	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
8	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
10	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
11	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv830891	chr7:5726301-5895460	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1028601	chr7:5748982-5919098	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
15	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
16	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
17	nsv464293	chr7:5778796-5891221	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv464294	chr7:5778796-5891221	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv605987	chr7:5778796-5891221	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	esv2764038	chr7:5785999-5893967	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv464296	chr7:5792745-5850642	Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv605988	chr7:5792745-5850642	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv471315	chr7:5792745-5891221	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	nsv605989	chr7:5794220-5891221	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	nsv1020103	chr7:5794220-5893955	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	esv3326694	chr7:5795518-5852599	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	esv3375120	chr7:5795699-5852633	Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5762000-5820400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:5781400-5816800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:5784000-5819600	Weak transcription	Fetal Heart	heart
4	chr7:5785200-5807000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:5790400-5804600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:5790800-5820400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:5792600-5816600	Weak transcription	Right Ventricle	heart
8	chr7:5792800-5813400	Weak transcription	Small Intestine	intestine
9	chr7:5792800-5813600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:5792800-5820000	Weak transcription	Fetal Kidney	kidney
11	chr7:5792800-5820200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:5792800-5820200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:5792800-5820200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:5794200-5806800	Weak transcription	Pancreas	Pancrea
15	chr7:5794400-5807400	Weak transcription	Gastric	stomach
16	chr7:5795200-5800800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:5795200-5800800	Strong transcription	Dnd41	blood
18	chr7:5795200-5812800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:5795400-5813200	Weak transcription	HMEC	breast
20	chr7:5795600-5805800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:5795600-5806400	Weak transcription	Hela-S3	cervix
22	chr7:5795600-5806800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:5795600-5807000	Weak transcription	Psoas Muscle	Psoas
24	chr7:5796600-5800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:5797000-5801000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:5797000-5807200	Weak transcription	K562	blood
27	chr7:5797400-5801000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr7:5798000-5800800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:5798200-5800800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:5798200-5800800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:5798400-5800800	Strong transcription	Left Ventricle	heart
32	chr7:5798800-5804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:5798800-5818800	Weak transcription	Brain Germinal Matrix	brain
34	chr7:5798800-5820400	Weak transcription	Esophagus	oesophagus
35	chr7:5799000-5801800	Weak transcription	Colonic Mucosa	Colon
36	chr7:5799000-5803200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:5799000-5804800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:5799000-5804800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:5799000-5804800	Weak transcription	Aorta	Aorta
40	chr7:5799000-5805000	Weak transcription	NH-A	brain
41	chr7:5799000-5805600	Weak transcription	NHLF	lung
42	chr7:5799000-5806000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:5799000-5806800	Weak transcription	Adipose Nuclei	Adipose
44	chr7:5799000-5806800	Weak transcription	Ovary	ovary
45	chr7:5799200-5804800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:5799200-5805800	Weak transcription	A549	lung
47	chr7:5799200-5805800	Weak transcription	HepG2	liver
48	chr7:5799200-5806000	Weak transcription	HUVEC	blood vessel
49	chr7:5799200-5806200	Weak transcription	Brain Angular Gyrus	brain
50	chr7:5799200-5806200	Weak transcription	Brain Inferior Temporal Lobe	brain

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