Variant report

Variant	rs3106164
Chromosome Location	chr6:160850273-160850274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:160527777..160530096-chr6:160849436..160852086,2	K562	blood:
2	chr6:160838522..160841226-chr6:160849057..160850823,2	K562	blood:
3	chr6:160845181..160849132-chr6:160849352..160851032,3	K562	blood:

Variant related genes	Relation type
ENSG00000270949	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10455782	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10945673	0.86[GIH][hapmap]
rs1810126	0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2048327	0.95[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2063346	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2063347	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs2292334	0.95[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2661839	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088442	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs3106162	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs3123636	0.91[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs388170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3918285	0.95[CEU][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs3918286	0.95[CEU][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6914575	0.86[GIH][hapmap]
rs7758229	0.91[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7769879	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs9346817	0.86[GIH][hapmap]
rs9355288	0.94[EUR][1000 genomes]
rs9355803	0.86[GIH][hapmap]
rs9355804	0.86[GIH][hapmap]
rs9365164	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.93[EUR][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	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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 target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv886810	chr6:160700769-160897872	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv1020357	chr6:160849895-160883394	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3106164	SLC22A3	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160818600-160876800	Weak transcription	Esophagus	oesophagus
2	chr6:160843800-160851400	Weak transcription	Fetal Brain Male	brain
3	chr6:160847400-160851000	Enhancers	Ovary	ovary
4	chr6:160847400-160852000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:160847600-160851000	Enhancers	Fetal Muscle Leg	muscle
6	chr6:160847800-160850400	Enhancers	Left Ventricle	heart
7	chr6:160847800-160850800	Enhancers	Fetal Muscle Trunk	muscle
8	chr6:160847800-160850800	Enhancers	Psoas Muscle	Psoas
9	chr6:160847800-160851000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:160847800-160853200	Enhancers	Adipose Nuclei	Adipose
11	chr6:160848000-160850600	Enhancers	Right Atrium	heart
12	chr6:160848000-160853000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:160848200-160851000	Enhancers	Rectal Smooth Muscle	rectum
14	chr6:160848200-160851600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:160848400-160850800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:160848400-160851800	Enhancers	Colon Smooth Muscle	Colon
17	chr6:160848600-160850800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:160848600-160851600	Weak transcription	Brain Germinal Matrix	brain
19	chr6:160848600-160856800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:160848800-160850400	Weak transcription	A549	lung
21	chr6:160848800-160851600	Weak transcription	Brain Substantia Nigra	brain
22	chr6:160848800-160851800	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:160849200-160851400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:160849400-160850600	Weak transcription	Fetal Stomach	stomach
25	chr6:160849400-160851800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:160849400-160866200	Weak transcription	Lung	lung
27	chr6:160849600-160850400	Weak transcription	Aorta	Aorta
28	chr6:160849600-160851600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:160849600-160851600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:160849600-160851600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:160849600-160851600	Weak transcription	Fetal Lung	lung
32	chr6:160849600-160851600	Weak transcription	Osteobl	bone
33	chr6:160849600-160851800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:160849600-160851800	Weak transcription	HSMM	muscle
35	chr6:160849600-160851800	Weak transcription	HSMMtube	muscle
36	chr6:160849600-160852800	Weak transcription	NHEK	skin
37	chr6:160849600-160858400	Weak transcription	Liver	Liver
38	chr6:160849800-160850400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:160849800-160850400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr6:160849800-160851000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:160849800-160852000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr6:160850000-160850800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:160850000-160850800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:160850000-160850800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:160850000-160850800	Enhancers	Placenta	Placenta
46	chr6:160850000-160850800	Enhancers	Gastric	stomach
47	chr6:160850000-160851000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:160850000-160851000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:160850000-160851400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:160850000-160852000	Enhancers	H1 Cell Line	embryonic stem cell

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