Variant report

Variant	rs59754974
Chromosome Location	chr6:86372702-86372703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86370760-86381789	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86360455..86373602-chr6:86382637..86391992,19	MCF-7	breast:
2	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5E-2	chr6:86371217-86374239	NONHSAT113850

Variant related genes	Relation type
PKMP3	TF binding region
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs56743649	0.82[AFR][1000 genomes]
rs60437369	0.82[AFR][1000 genomes]
rs60564421	0.88[AFR][1000 genomes]
rs73481340	0.82[AFR][1000 genomes]
rs73481343	0.82[AFR][1000 genomes]
rs73481361	0.82[AFR][1000 genomes]
rs73481395	0.82[AFR][1000 genomes]
rs73481397	0.82[AFR][1000 genomes]
rs73483557	0.82[AFR][1000 genomes]
rs73483572	0.82[AFR][1000 genomes]
rs73483573	0.82[AFR][1000 genomes]
rs73483583	0.82[AFR][1000 genomes]
rs73483591	0.85[AFR][1000 genomes]
rs73485417	0.94[AFR][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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
5	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354200-86374400	Weak transcription	Left Ventricle	heart
2	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:86355200-86377000	Weak transcription	Thymus	Thymus
4	chr6:86355200-86380400	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
6	chr6:86360600-86375000	Weak transcription	Brain Germinal Matrix	brain
7	chr6:86366800-86377800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:86367800-86375200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:86367800-86381800	Weak transcription	Lung	lung
10	chr6:86368200-86377600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:86368200-86384800	Weak transcription	Right Ventricle	heart
12	chr6:86368400-86374400	Weak transcription	Fetal Thymus	thymus
13	chr6:86368400-86375000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:86368600-86382600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:86368600-86384800	Weak transcription	Spleen	Spleen
16	chr6:86368800-86380200	Weak transcription	Adipose Nuclei	Adipose
17	chr6:86370000-86373400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:86370200-86375000	Weak transcription	Brain Substantia Nigra	brain
19	chr6:86370200-86378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:86370200-86379800	Weak transcription	Gastric	stomach
21	chr6:86370200-86384400	Weak transcription	Esophagus	oesophagus
22	chr6:86370200-86384400	Weak transcription	Fetal Brain Male	brain
23	chr6:86370200-86385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:86370400-86373200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:86370400-86373200	Weak transcription	Ovary	ovary
26	chr6:86370400-86373200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:86370400-86375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:86370400-86375000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:86370400-86375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:86370400-86375000	Weak transcription	Brain Angular Gyrus	brain
31	chr6:86370400-86375000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:86370400-86380200	Weak transcription	Fetal Lung	lung
33	chr6:86370400-86382600	Weak transcription	A549	lung
34	chr6:86370400-86383200	Weak transcription	Aorta	Aorta
35	chr6:86370400-86384400	Weak transcription	Psoas Muscle	Psoas
36	chr6:86370400-86385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:86370400-86386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:86370600-86377800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:86370600-86379400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:86370600-86379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:86370600-86379600	Weak transcription	Osteobl	bone
42	chr6:86370600-86379800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:86370600-86379800	Weak transcription	NHLF	lung
44	chr6:86370800-86384600	Weak transcription	HSMMtube	muscle
45	chr6:86371400-86377800	Strong transcription	Fetal Stomach	stomach
46	chr6:86371400-86383400	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:86371600-86376400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:86371800-86375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:86371800-86375800	Strong transcription	Fetal Brain Female	brain
50	chr6:86371800-86376800	Strong transcription	Fetal Muscle Leg	muscle

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