Variant report

Variant	rs563406132
Chromosome Location	chr6:15248493-15248494
allele	G/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	CTCF	chr6:15248420-15248570	AG09309	skin:	n/a	n/a
2	CHD2	chr6:15247900-15249524	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:15247900-15248597	K562	blood:	n/a	n/a
4	POLR2A	chr6:15247950-15249674	H1-neurons	neurons:	n/a	n/a
5	CTCF	chr6:15248390-15248590	Pancreas_OC	pancreas:	n/a	n/a
6	YY1	chr6:15248305-15248625	GM12891	blood:	n/a	n/a
7	CREB1	chr6:15247870-15249858	GM12878	blood:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
8	CTCF	chr6:15248440-15248590	AoAF	blood vessel:	n/a	n/a
9	CREB1	chr6:15248096-15249493	A549	lung:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
10	CTCF	chr6:15248460-15248610	GM12866	blood:	n/a	n/a
11	ZBTB7A	chr6:15248129-15249179	K562	blood:	n/a	chr6:15248701-15248710
12	POLR2A	chr6:15247921-15248583	K562	blood:	n/a	n/a
13	CREB1	chr6:15248155-15249672	HepG2	liver:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
14	CREB1	chr6:15247845-15250008	K562	blood:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
15	YY1	chr6:15248132-15248537	GM12892	blood:	n/a	n/a
16	CTCF	chr6:15248440-15248590	GM12875	blood:	n/a	n/a
17	MAX	chr6:15247952-15249665	HepG2	liver:	n/a	n/a
18	SMARCB1	chr6:15248060-15249597	Hela-S3	cervix:	n/a	n/a
19	HDAC2	chr6:15248191-15248641	HepG2	liver:	n/a	n/a
20	CTCF	chr6:15248420-15248570	HPAF	blood vessel:	n/a	n/a
21	POLR2A	chr6:15248023-15249417	K562	blood:	n/a	n/a
22	CTCF	chr6:15248440-15248590	AG09309	skin:	n/a	n/a
23	CTCF	chr6:15248460-15248610	GM12873	blood:	n/a	n/a
24	CTCF	chr6:15248310-15248611	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr6:15248420-15248570	HA-sp	spinal cord:	n/a	n/a
26	CTCF	chr6:15248440-15248590	Caco-2	colon:	n/a	n/a
27	ZBTB7A	chr6:15248291-15249161	HepG2	liver:	n/a	chr6:15248701-15248710
28	SIN3AK20	chr6:15247987-15248560	K562	blood:	n/a	n/a
29	REST	chr6:15247989-15248537	HL-60	blood:	n/a	n/a
30	RAD21	chr6:15244609-15249567	IMR90	lung:	n/a	chr6:15248721-15248734 chr6:15249188-15249197
31	E2F6	chr6:15248188-15249536	K562	blood:	n/a	chr6:15248973-15248982 chr6:15248906-15248917 chr6:15248702-15248711 chr6:15248975-15248984 chr6:15249022-15249031
32	CTCF	chr6:15248370-15249436	K562	blood:	n/a	chr6:15249189-15249198 chr6:15248720-15248733
33	POLR2A	chr6:15248043-15249620	GM12892	blood:	n/a	n/a
34	POLR2A	chr6:15248078-15248530	GM12878	blood:	n/a	n/a
35	CTCF	chr6:15248440-15248590	NHEK	skin:	n/a	n/a
36	MYC	chr6:15248065-15249572	NB4	blood:	n/a	n/a
37	CTCF	chr6:15248420-15248570	HepG2	liver:	n/a	n/a
38	E2F4	chr6:15248125-15249314	K562	blood:	n/a	chr6:15248973-15248982 chr6:15248702-15248711 chr6:15248975-15248984 chr6:15249022-15249031
39	HEY1	chr6:15247951-15248555	K562	blood:	n/a	n/a
40	UBTF	chr6:15247953-15249575	K562	blood:	n/a	n/a
41	CTCF	chr6:15248460-15248610	GM12871	blood:	n/a	n/a
42	MAX	chr6:15247957-15248647	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:15248088-15249623	GM19099	blood:	n/a	n/a
44	YY1	chr6:15248065-15249053	K562	blood:	n/a	chr6:15248723-15248737
45	HCFC1	chr6:15244775-15250295	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr6:15248420-15248570	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr6:15248424-15248597	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr6:15248480-15248630	RPTEC	kidney:	n/a	n/a
49	ZBTB7A	chr6:15248322-15248590	HepG2	liver:	n/a	n/a
50	CTCF	chr6:15248380-15248530	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:14695043..14697656-chr6:15246930..15248844,2	K562	blood:
2	chr6:15247857..15248661-chr6:15441250..15442133,2	MCF-7	breast:
3	chr6:15085986..15094450-chr6:15243173..15249347,32	MCF-7	breast:
4	chr1:155278025..155278903-chr6:15248328..15249078,2	Hela-S3	cervix:
5	chr6:15238350..15240596-chr6:15246578..15248795,2	MCF-7	breast:
6	chr6:15088518..15090840-chr6:15243708..15248817,8	MCF-7	breast:
7	chr18:57566476..57568620-chr6:15247479..15249980,2	K562	blood:
8	chr6:15248004..15250330-chr6:15324617..15327935,3	K562	blood:
9	chr12:54673793..54674774-chr6:15248174..15248787,2	Hela-S3	cervix:
10	chr6:15087836..15090279-chr6:15247303..15249952,4	K562	blood:
11	chr6:15090854..15092609-chr6:15247191..15248815,2	MCF-7	breast:
12	chr6:15147856..15151805-chr6:15244004..15248641,4	MCF-7	breast:
13	chr6:15087697..15092455-chr6:15243972..15249952,11	K562	blood:
14	chr6:15247440..15249791-chr6:15324617..15327427,3	K562	blood:

Variant related genes	Relation type
JARID2	TF binding region
ENSG00000271888	TF binding region
ENSG00000264687	Chromatin interaction
ENSG00000141682	Chromatin interaction
ENSG00000201519	Chromatin interaction
ENSG00000094916	Chromatin interaction
ENSG00000234261	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000135486	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1818166	chr6:15247393-15250052	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv3426622	chr6:15247498-15250346	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3511820	chr6:15247723-15249971	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv3511821	chr6:15247723-15249971	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3437390	chr6:15248023-15249771	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv13446	chr6:15248316-15249040	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15243600-15250200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:15244000-15250000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:15244200-15249400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:15244200-15249800	Active TSS	Rectal Smooth Muscle	rectum
5	chr6:15244400-15249200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:15244400-15249400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:15244400-15249600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr6:15244400-15250200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:15244400-15250400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:15244600-15249200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:15244600-15249200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:15244600-15249200	Active TSS	Duodenum Mucosa	Duodenum
13	chr6:15244600-15249200	Active TSS	NH-A	brain
14	chr6:15244600-15249200	Active TSS	Osteobl	bone
15	chr6:15244600-15249400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:15244600-15249400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:15244600-15249400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:15244600-15249400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:15244600-15249400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:15244600-15249400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:15244600-15249400	Active TSS	Brain Anterior Caudate	brain
22	chr6:15244600-15249400	Active TSS	Fetal Intestine Large	intestine
23	chr6:15244600-15249400	Active TSS	Thymus	Thymus
24	chr6:15244600-15249400	Active TSS	HSMM	muscle
25	chr6:15244600-15249600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:15244600-15249600	Active TSS	Brain Angular Gyrus	brain
27	chr6:15244600-15249600	Active TSS	Right Ventricle	heart
28	chr6:15244600-15249800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:15244600-15249800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:15244600-15249800	Active TSS	Ovary	ovary
31	chr6:15244600-15249800	Active TSS	Psoas Muscle	Psoas
32	chr6:15244600-15250000	Active TSS	NHLF	lung
33	chr6:15244600-15250200	Active TSS	A549	lung
34	chr6:15244600-15250400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:15244800-15249200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:15244800-15249200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr6:15244800-15249200	Active TSS	Left Ventricle	heart
38	chr6:15244800-15249200	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:15244800-15249400	Active TSS	Brain Substantia Nigra	brain
40	chr6:15244800-15249400	Active TSS	Fetal Kidney	kidney
41	chr6:15244800-15249400	Active TSS	Fetal Lung	lung
42	chr6:15244800-15249400	Active TSS	Lung	lung
43	chr6:15244800-15249600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:15244800-15249600	Active TSS	Gastric	stomach
45	chr6:15244800-15249600	Active TSS	HSMMtube	muscle
46	chr6:15244800-15249800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:15244800-15249800	Active TSS	Aorta	Aorta
48	chr6:15244800-15249800	Active TSS	Esophagus	oesophagus
49	chr6:15244800-15250000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:15245000-15248600	Active TSS	Spleen	Spleen

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