Variant report

Variant	rs169790
Chromosome Location	chr6:11714291-11714292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11707605..11709932-chr6:11714222..11716200,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEDD9-2	chr6:11713908-11714745	NONHSAT107762
2	lnc-NEDD9-2	chr6:11714187-11714745	NONHSAT107763

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs172403	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210891	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210893	1.00[JPT][hapmap]
rs210900	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs210907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs210909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs210912	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs210916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs210923	1.00[AFR][1000 genomes]
rs210927	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210928	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210929	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210932	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs210934	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2743952	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs849011	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462637	chr6:11710554-11733777	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600990	chr6:11710554-11733777	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11704200-11714800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:11708200-11714800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:11708400-11716800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:11709000-11714800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:11709000-11715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:11709000-11716400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:11709800-11716400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:11710000-11715200	Enhancers	Fetal Thymus	thymus
9	chr6:11710800-11731000	Weak transcription	Gastric	stomach
10	chr6:11711200-11715400	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:11711200-11731000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:11711400-11715400	Enhancers	Primary B cells from cord blood	blood
13	chr6:11711400-11718400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:11711400-11719200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:11711600-11715200	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:11711600-11731800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:11711800-11715000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:11711800-11715800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:11712200-11715800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:11712200-11718400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:11712400-11721000	Weak transcription	HSMM	muscle
22	chr6:11712600-11716000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:11712800-11714400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:11712800-11714800	Weak transcription	Right Atrium	heart
25	chr6:11712800-11716400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:11712800-11716800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:11713000-11714600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:11713000-11715200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:11713200-11716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:11713200-11721000	Weak transcription	HMEC	breast
31	chr6:11713400-11714800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:11713400-11714800	Weak transcription	Spleen	Spleen
33	chr6:11713400-11723000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:11713400-11724600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:11713600-11718400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:11713600-11718600	Weak transcription	NHLF	lung
37	chr6:11713600-11727600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:11713800-11714800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:11713800-11714800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:11713800-11723200	Weak transcription	HSMMtube	muscle
41	chr6:11714000-11719200	Weak transcription	NHEK	skin
42	chr6:11714200-11714400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:11714200-11714800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr6:11714200-11715000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:11714200-11715200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr6:11714200-11715600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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