Variant report

Variant	rs559146952
Chromosome Location	chr6:44238411-44238412
allele	C/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	CTCF	chr6:44238400-44238550	GM12874	blood:	n/a	n/a
2	REST	chr6:44237315-44239608	H1-neurons	neurons:	n/a	chr6:44238836-44238849 chr6:44238124-44238137 chr6:44238436-44238446 chr6:44237917-44237927
3	ZBTB7A	chr6:44238264-44239049	ECC-1	luminal epithelium:	n/a	chr6:44238463-44238472 chr6:44238629-44238636
4	SIN3A	chr6:44238394-44238961	H1-hESC	embryonic stem cell:	n/a	n/a
5	EP300	chr6:44238361-44238818	H1-hESC	embryonic stem cell:	n/a	chr6:44238639-44238655
6	SIN3AK20	chr6:44238321-44238905	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:44237786-44239191	H1-neurons	neurons:	n/a	n/a
8	ZBTB7A	chr6:44238303-44238938	K562	blood:	n/a	chr6:44238463-44238472 chr6:44238629-44238636
9	REST	chr6:44238388-44239018	SK-N-SH	brain:	n/a	chr6:44238836-44238849 chr6:44238436-44238446
10	ZBTB7A	chr6:44238376-44239000	K562	blood:	n/a	chr6:44238463-44238472 chr6:44238629-44238636
11	REST	chr6:44238306-44239041	ECC-1	luminal epithelium:	n/a	chr6:44238836-44238849 chr6:44238436-44238446
12	MAZ	chr6:44238298-44239163	IMR90	lung:	n/a	chr6:44238381-44238391 chr6:44239104-44239114
13	POLR2A	chr6:44237840-44239211	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44231911..44234847-chr6:44237510..44240187,2	MCF-7	breast:
2	chr6:44237771..44241790-chr6:44264717..44266725,3	MCF-7	breast:

Variant related genes	Relation type
NFKBIE	TF binding region
TMEM151B	TF binding region
ENSG00000272442	TF binding region
ENSG00000146232	Chromatin interaction
ENSG00000146221	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
12	esv3358306	chr6:44236999-44239947	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	esv3508275	chr6:44237449-44239997	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	esv3508276	chr6:44237449-44239997	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	esv3395844	chr6:44237774-44239722	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44236400-44238800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:44237000-44239200	Bivalent Enhancer	HUVEC	blood vessel
3	chr6:44237600-44238800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:44237600-44239000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:44237800-44238600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:44237800-44238800	Bivalent/Poised TSS	Thymus	Thymus
7	chr6:44237800-44239000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:44237800-44239200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:44237800-44239200	Active TSS	Brain Angular Gyrus	brain
10	chr6:44238000-44238800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:44238000-44238800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:44238000-44238800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:44238000-44238800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:44238000-44238800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:44238000-44238800	Enhancers	Fetal Brain Male	brain
16	chr6:44238000-44238800	Active TSS	Right Atrium	heart
17	chr6:44238000-44239000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:44238000-44239000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:44238000-44239000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:44238000-44239000	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr6:44238000-44239000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:44238000-44239000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:44238000-44239000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:44238000-44239000	Active TSS	Brain Germinal Matrix	brain
25	chr6:44238000-44239000	Active TSS	Fetal Brain Female	brain
26	chr6:44238000-44239000	Active TSS	Psoas Muscle	Psoas
27	chr6:44238000-44239000	Active TSS	Right Ventricle	heart
28	chr6:44238000-44239000	Bivalent/Poised TSS	HepG2	liver
29	chr6:44238000-44239200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:44238000-44239200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:44238000-44239200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr6:44238000-44239200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:44238000-44239200	Active TSS	Brain Anterior Caudate	brain
34	chr6:44238000-44239400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:44238000-44240800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:44238200-44238600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:44238200-44238600	Active TSS	Pancreas	Pancrea
38	chr6:44238200-44238600	Bivalent/Poised TSS	HSMM	muscle
39	chr6:44238200-44238800	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:44238200-44238800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr6:44238200-44238800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:44238200-44238800	Active TSS	Aorta	Aorta
43	chr6:44238200-44239000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr6:44238200-44239000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:44238200-44239000	Active TSS	Ovary	ovary
46	chr6:44238200-44239400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:44238400-44238600	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
48	chr6:44238400-44238600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:44238400-44238600	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr6:44238400-44238800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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