Variant report

Variant	rs202041
Chromosome Location	chr6:13288425-13288426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13287558-13289732	GM18505	blood:	n/a	n/a
2	POLR2A	chr6:13288389-13289015	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:13286577-13289782	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:13284901-13290945	K562	blood:	n/a	n/a
5	POLR2A	chr6:13288363-13289804	K562	blood:	n/a	n/a
6	POLR2A	chr6:13288385-13289047	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:13287692-13288561	GM12878	blood:	n/a	n/a
8	PML	chr6:13287786-13289167	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:13287591-13289738	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:13287126-13290476	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:13287514-13289720	GM19193	blood:	n/a	n/a
12	POLR2A	chr6:13288387-13289768	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:13287396-13289874	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:13288392-13289741	GM12891	blood:	n/a	n/a
15	MTA3	chr6:13287876-13291052	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:13287490-13289950	GM12892	blood:	n/a	n/a
17	ZNF384	chr6:13288154-13288587	K562	blood:	n/a	n/a
18	POLR2A	chr6:13288388-13289786	K562	blood:	n/a	n/a
19	POLR2A	chr6:13288298-13288650	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr6:13284889-13290972	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:13288372-13289799	HL-60	blood:	n/a	n/a
22	POLR2A	chr6:13286946-13289896	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:13287500-13289829	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:13287412-13288458	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFATC1	chr6:13287802-13290134	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:13288395-13288727	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:13287681-13289800	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:13288422-13289682	GM15510	blood:	n/a	n/a
29	POLR2A	chr6:13288383-13288875	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:13287650-13289766	GM12892	blood:	n/a	n/a
32	NFATC1	chr6:13288425-13288975	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:13287696-13289813	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
2	chr6:13272685..13275870-chr6:13286064..13289898,4	K562	blood:
3	chr6:13287888..13289538-chr6:13307383..13309880,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000112137	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs202036	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202039	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384730	0.81[EUR][1000 genomes]
rs398151	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs412787	0.81[EUR][1000 genomes]
rs442614	0.81[EUR][1000 genomes]
rs543645	0.93[ASN][1000 genomes]
rs561549	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202041	RP1-257A7.5	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13270200-13291600	Weak transcription	HSMM	muscle
2	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
3	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
4	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
5	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:13280000-13289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:13280000-13292600	Weak transcription	NHLF	lung
9	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:13282800-13289400	Strong transcription	Right Ventricle	heart
11	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:13283600-13288600	Strong transcription	Aorta	Aorta
13	chr6:13283600-13289600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:13285000-13289600	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
18	chr6:13285800-13288600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:13285800-13288800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr6:13285800-13289800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
22	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
23	chr6:13286000-13288800	ZNF genes & repeats	Fetal Stomach	stomach
24	chr6:13286400-13288800	ZNF genes & repeats	HepG2	liver
25	chr6:13286400-13289000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:13286600-13288600	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr6:13286600-13288600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
28	chr6:13286600-13288600	ZNF genes & repeats	K562	blood
29	chr6:13286600-13288800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr6:13286600-13289000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr6:13286600-13291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
33	chr6:13286800-13288600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr6:13286800-13288600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13286800-13288600	ZNF genes & repeats	Fetal Brain Female	brain
36	chr6:13286800-13288600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr6:13286800-13288800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr6:13286800-13288800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:13286800-13289400	ZNF genes & repeats	Fetal Intestine Large	intestine
40	chr6:13287000-13288800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:13287000-13288800	ZNF genes & repeats	Lung	lung
42	chr6:13287000-13289200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:13287000-13289600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
44	chr6:13287000-13289800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:13287000-13289800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr6:13287000-13289800	Strong transcription	Gastric	stomach
47	chr6:13287000-13289800	ZNF genes & repeats	Thymus	Thymus
48	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:13287200-13288600	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr6:13287200-13288800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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