Variant report

Variant	rs678409
Chromosome Location	chr6:74299575-74299576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74220978..74235626-chr6:74283533..74299827,68	K562	blood:
2	chr6:74289354..74292208-chr6:74297018..74299790,3	MCF-7	breast:
3	chr6:74293866..74296330-chr6:74299032..74301515,2	K562	blood:

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12192512	0.89[EUR][1000 genomes]
rs12212323	0.88[EUR][1000 genomes]
rs12212380	0.86[EUR][1000 genomes]
rs1245333	0.92[EUR][1000 genomes]
rs1303141	0.92[EUR][1000 genomes]
rs1691343	0.92[EUR][1000 genomes]
rs1691344	0.89[EUR][1000 genomes]
rs1691347	0.92[EUR][1000 genomes]
rs1703463	0.90[EUR][1000 genomes]
rs1741891	0.91[EUR][1000 genomes]
rs1741898	0.92[EUR][1000 genomes]
rs382038	0.81[EUR][1000 genomes]
rs382041	0.93[EUR][1000 genomes]
rs395996	0.93[EUR][1000 genomes]
rs428944	0.85[EUR][1000 genomes]
rs435132	0.93[EUR][1000 genomes]
rs453979	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473473	0.90[EUR][1000 genomes]
rs475459	0.92[EUR][1000 genomes]
rs476996	0.92[EUR][1000 genomes]
rs478836	0.86[EUR][1000 genomes]
rs480714	0.92[EUR][1000 genomes]
rs480871	0.92[EUR][1000 genomes]
rs485802	0.91[EUR][1000 genomes]
rs535502	0.82[EUR][1000 genomes]
rs546134	0.91[EUR][1000 genomes]
rs549892	0.91[EUR][1000 genomes]
rs560797	0.92[EUR][1000 genomes]
rs565535	0.90[EUR][1000 genomes]
rs573753	0.91[EUR][1000 genomes]
rs583443	0.82[EUR][1000 genomes]
rs605567	0.92[EUR][1000 genomes]
rs612800	0.91[EUR][1000 genomes]
rs615052	0.91[EUR][1000 genomes]
rs626323	0.88[EUR][1000 genomes]
rs628038	0.91[EUR][1000 genomes]
rs670248	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676464	0.82[EUR][1000 genomes]
rs970091	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS 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 miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74289400-74302200	Weak transcription	Spleen	Spleen
2	chr6:74289400-74304000	Weak transcription	Right Ventricle	heart
3	chr6:74289600-74309600	Weak transcription	Lung	lung
4	chr6:74289600-74323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:74289800-74301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:74290600-74305800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:74290600-74318400	Weak transcription	Small Intestine	intestine
8	chr6:74290600-74338800	Weak transcription	Ovary	ovary
9	chr6:74291000-74307200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:74291000-74315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:74291000-74323600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:74295200-74302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:74295200-74303200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:74295200-74321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:74296000-74317200	Weak transcription	Fetal Brain Female	brain
16	chr6:74296200-74317800	Weak transcription	Colonic Mucosa	Colon
17	chr6:74296200-74317800	Weak transcription	Gastric	stomach
18	chr6:74296200-74322200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:74296200-74322400	Weak transcription	Brain Germinal Matrix	brain
20	chr6:74296200-74332000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:74296400-74302600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:74296400-74302600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:74296400-74302600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:74296400-74302600	Weak transcription	Thymus	Thymus
25	chr6:74296400-74303200	Weak transcription	Fetal Stomach	stomach
26	chr6:74296400-74307200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:74296400-74307200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:74296400-74307400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:74296400-74309000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:74296400-74309000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:74296400-74316000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:74296400-74316400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:74296400-74318400	Weak transcription	Aorta	Aorta
34	chr6:74296400-74318400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:74296400-74325800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:74296400-74354800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:74296400-74354800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:74296400-74355000	Weak transcription	Fetal Brain Male	brain
39	chr6:74296600-74299800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:74296600-74302200	Weak transcription	Left Ventricle	heart
41	chr6:74296600-74302200	Weak transcription	NHDF-Ad	bronchial
42	chr6:74296600-74302600	Weak transcription	Adipose Nuclei	Adipose
43	chr6:74296600-74302600	Weak transcription	Fetal Intestine Small	intestine
44	chr6:74296600-74302600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:74296600-74302600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:74296600-74303200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:74296600-74303600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:74296600-74304200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:74296600-74304200	Weak transcription	NHLF	lung
50	chr6:74296600-74307400	Weak transcription	Brain Angular Gyrus	brain

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