Variant report

Variant	rs35988746
Chromosome Location	chr6:86374198-86374199
allele	A/G
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	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:
2	chr6:86369831..86371356-chr6:86373551..86376198,2	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
ENSG00000220563	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13194512	0.83[EUR][1000 genomes]
rs13198956	0.83[EUR][1000 genomes]
rs13202606	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16876340	0.83[EUR][1000 genomes]
rs16876385	0.83[EUR][1000 genomes]
rs1793	0.83[EUR][1000 genomes]
rs34239697	0.91[EUR][1000 genomes]
rs34898046	0.83[EUR][1000 genomes]
rs34936540	0.83[EUR][1000 genomes]
rs35121980	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35367106	0.91[EUR][1000 genomes]
rs35694036	0.83[EUR][1000 genomes]
rs35712823	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36088473	0.83[EUR][1000 genomes]
rs3734442	0.83[EUR][1000 genomes]
rs3900740	0.83[EUR][1000 genomes]
rs4707206	0.83[EUR][1000 genomes]
rs4707213	0.83[EUR][1000 genomes]
rs55648312	0.83[EUR][1000 genomes]
rs55810446	0.83[EUR][1000 genomes]
rs67493405	0.83[EUR][1000 genomes]
rs6906121	0.83[EUR][1000 genomes]
rs6909402	0.83[EUR][1000 genomes]
rs6909654	0.83[EUR][1000 genomes]
rs71570764	0.83[EUR][1000 genomes]
rs71570766	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7738371	0.83[EUR][1000 genomes]
rs7740830	0.83[EUR][1000 genomes]
rs7771577	0.83[EUR][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:64 , 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	chr6:86370200-86375000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:86370200-86378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:86370200-86379800	Weak transcription	Gastric	stomach
20	chr6:86370200-86384400	Weak transcription	Esophagus	oesophagus
21	chr6:86370200-86384400	Weak transcription	Fetal Brain Male	brain
22	chr6:86370200-86385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:86370400-86375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:86370400-86375000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:86370400-86375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:86370400-86375000	Weak transcription	Brain Angular Gyrus	brain
27	chr6:86370400-86375000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:86370400-86380200	Weak transcription	Fetal Lung	lung
29	chr6:86370400-86382600	Weak transcription	A549	lung
30	chr6:86370400-86383200	Weak transcription	Aorta	Aorta
31	chr6:86370400-86384400	Weak transcription	Psoas Muscle	Psoas
32	chr6:86370400-86385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:86370400-86386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:86370600-86377800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:86370600-86379400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:86370600-86379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:86370600-86379600	Weak transcription	Osteobl	bone
38	chr6:86370600-86379800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:86370600-86379800	Weak transcription	NHLF	lung
40	chr6:86370800-86384600	Weak transcription	HSMMtube	muscle
41	chr6:86371400-86377800	Strong transcription	Fetal Stomach	stomach
42	chr6:86371400-86383400	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:86371600-86376400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:86371800-86375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:86371800-86375800	Strong transcription	Fetal Brain Female	brain
46	chr6:86371800-86376800	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:86372000-86374200	Weak transcription	Fetal Intestine Small	intestine
48	chr6:86372000-86379600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:86372200-86380400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:86372400-86375000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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