Variant report

Variant	rs60005089
Chromosome Location	chr6:28279474-28279475
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28278749..28286420-chr6:28298924..28309589,20	K562	blood:
2	chr6:28278690..28281090-chr6:28292415..28293983,2	K562	blood:
3	chr6:28278744..28280710-chr6:28315124..28318113,2	K562	blood:
4	chr6:28279292..28281090-chr6:28292483..28294550,2	K562	blood:
5	chr6:28252016..28254141-chr6:28279359..28281399,2	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1150682	1.00[EUR][1000 genomes]
rs1225593	1.00[EUR][1000 genomes]
rs1619221	1.00[EUR][1000 genomes]
rs175955	1.00[EUR][1000 genomes]
rs1770132	1.00[EUR][1000 genomes]
rs203867	1.00[EUR][1000 genomes]
rs203874	1.00[EUR][1000 genomes]
rs2622318	1.00[EUR][1000 genomes]
rs34223404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55826226	1.00[EUR][1000 genomes]
rs57481919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57672617	1.00[EUR][1000 genomes]
rs73740585	1.00[EUR][1000 genomes]
rs73740597	1.00[EUR][1000 genomes]
rs73740600	1.00[EUR][1000 genomes]
rs73740605	1.00[EUR][1000 genomes]
rs73740628	1.00[EUR][1000 genomes]
rs73740636	1.00[EUR][1000 genomes]
rs73742514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742531	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
4	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
10	chr6:28269400-28280800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:28269800-28280000	Weak transcription	Left Ventricle	heart
12	chr6:28270000-28280800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:28270000-28290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:28270000-28291400	Weak transcription	Ovary	ovary
15	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
16	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
17	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
18	chr6:28270400-28279600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
26	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:28278400-28280000	Enhancers	HepG2	liver
28	chr6:28278600-28279600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:28278800-28279600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:28278800-28279600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28278800-28279600	Enhancers	GM12878-XiMat	blood
32	chr6:28279000-28279800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:28279000-28279800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr6:28279200-28279600	Enhancers	K562	blood
35	chr6:28279200-28280600	Weak transcription	Esophagus	oesophagus
36	chr6:28279400-28280600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:28279400-28280600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:28279400-28280800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:28279400-28280800	Weak transcription	Pancreas	Pancrea
40	chr6:28279400-28285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:28279400-28290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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