Variant report

Variant	rs9347511
Chromosome Location	chr6:161855785-161855786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161855024..161858360-chr6:161858723..161860898,4	MCF-7	breast:
2	chr6:161855223..161857273-chr6:161905432..161907491,2	MCF-7	breast:
3	chr3:161087670..161090609-chr6:161855286..161856788,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12661014	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2872894	0.86[EUR][1000 genomes]
rs4709525	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4709526	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62435941	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9346853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347510	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9347512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2752091	chr6:161592100-161855785	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
4	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv886819	chr6:161712035-162520133	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv886820	chr6:161712880-162184932	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv830854	chr6:161739926-161927515	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv518931	chr6:161793319-162406335	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv481861	chr6:161802883-162160197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1033192	chr6:161812419-161860010	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv886821	chr6:161812626-161859628	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1024921	chr6:161814295-161860636	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2761040	chr6:161814307-161860636	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv520078	chr6:161814907-161860010	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv605066	chr6:161814907-161860010	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv481930	chr6:161815297-161860058	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv605067	chr6:161816660-161860010	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1022345	chr6:161816661-161860010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1018065	chr6:161816661-161860169	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1018466	chr6:161816661-161860636	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv605068	chr6:161817168-161860010	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1023319	chr6:161817703-161860636	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv481981	chr6:161829077-162215745	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1015211	chr6:161836242-161860636	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv1033603	chr6:161844266-162001436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv481750	chr6:161850976-161996586	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9347511	SLC22A2	cis	parietal	SCAN
rs9347511	SNORA29	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161854600-161856200	Enhancers	NHLF	lung
2	chr6:161855000-161855800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:161855000-161856800	Enhancers	Fetal Stomach	stomach
4	chr6:161855200-161855800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:161855200-161855800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:161855200-161855800	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:161855200-161855800	Active TSS	Brain Hippocampus Middle	brain
8	chr6:161855200-161855800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:161855200-161855800	Flanking Active TSS	HSMM	muscle
10	chr6:161855200-161856000	Active TSS	Brain Anterior Caudate	brain
11	chr6:161855200-161856000	Active TSS	Brain Substantia Nigra	brain
12	chr6:161855200-161856000	Flanking Active TSS	NH-A	brain
13	chr6:161855200-161856000	Flanking Active TSS	NHDF-Ad	bronchial
14	chr6:161855200-161856400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:161855200-161856400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr6:161855200-161856400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:161855200-161856400	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:161855200-161856600	Active TSS	Psoas Muscle	Psoas
19	chr6:161855200-161856800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:161855200-161856800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:161855200-161856800	Enhancers	Fetal Lung	lung
22	chr6:161855200-161856800	Enhancers	NHEK	skin
23	chr6:161855200-161857000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:161855200-161857800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:161855200-161858000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:161855400-161855800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:161855400-161855800	Enhancers	Ovary	ovary
28	chr6:161855400-161855800	Enhancers	Right Atrium	heart
29	chr6:161855400-161855800	Flanking Active TSS	Osteobl	bone
30	chr6:161855400-161856000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:161855400-161856000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:161855400-161856000	Enhancers	Fetal Brain Male	brain
33	chr6:161855400-161856200	Enhancers	Left Ventricle	heart
34	chr6:161855400-161856200	Enhancers	Small Intestine	intestine
35	chr6:161855400-161856400	Active TSS	Aorta	Aorta
36	chr6:161855400-161856400	Flanking Active TSS	HSMMtube	muscle
37	chr6:161855400-161856600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:161855400-161856800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:161855400-161856800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:161855400-161856800	Enhancers	Fetal Intestine Large	intestine
41	chr6:161855400-161856800	Enhancers	Fetal Kidney	kidney
42	chr6:161855400-161856800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:161855400-161857000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:161855400-161857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:161855400-161857000	Enhancers	Fetal Muscle Leg	muscle
46	chr6:161855600-161855800	Active TSS	Adipose Nuclei	Adipose
47	chr6:161855600-161855800	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr6:161855600-161855800	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:161855600-161855800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:161855600-161855800	Active TSS	Stomach Smooth Muscle	stomach

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