Variant report

Variant	rs1115713
Chromosome Location	chr20:30135990-30135991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:30134609-30136067	GM12892	blood:	n/a	n/a
2	POLR2A	chr20:30134820-30136232	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr20:30134664-30136140	GM12892	blood:	n/a	n/a
4	POLR2A	chr20:30135520-30136008	GM12891	blood:	n/a	n/a
5	HEY1	chr20:30134700-30136259	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:30134743-30138182	HepG2	liver:	n/a	n/a
7	POLR2A	chr20:30134681-30136108	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr20:30134559-30136430	GM12878	blood:	n/a	n/a
9	POLR2A	chr20:30133203-30138254	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:30134674-30136161	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr20:30134595-30136319	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr20:30134676-30136447	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr20:30134750-30136184	GM12878	blood:	n/a	n/a
14	SIN3A	chr20:30134806-30136000	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr20:30134779-30136010	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr20:30134815-30136154	GM19099	blood:	n/a	n/a
17	POLR2A	chr20:30134715-30136410	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr20:30134784-30138055	K562	blood:	n/a	n/a
19	MXI1	chr20:30134573-30136325	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr20:30134669-30136053	GM12878	blood:	n/a	n/a
21	POLR2A	chr20:30134457-30137482	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr20:30134637-30136082	HepG2	liver:	n/a	n/a
23	POLR2A	chr20:30135951-30136353	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr20:30134580-30136322	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr20:30134680-30136095	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr20:30134669-30136097	PANC-1	pancreas:	n/a	n/a
27	HCFC1	chr20:30134560-30136439	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr20:30134620-30137051	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr20:30134666-30136258	U87	brain:	n/a	n/a
30	POLR2A	chr20:30134666-30136285	U87	brain:	n/a	n/a
31	POLR2A	chr20:30134716-30136066	GM12891	blood:	n/a	n/a
32	POLR2A	chr20:30134607-30136124	GM12892	blood:	n/a	n/a
33	POLR2A	chr20:30134720-30136075	HepG2	liver:	n/a	n/a
34	POLR2A	chr20:30134478-30136652	U87	brain:	n/a	n/a
35	POLR2A	chr20:30134521-30137860	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr20:30134613-30137987	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr20:30134739-30137834	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr20:30134795-30136074	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr20:30135779-30136076	GM12892	blood:	n/a	n/a
40	POLR2A	chr20:30134720-30136040	MCF-7	breast:	n/a	n/a
41	USF2	chr20:30134756-30136555	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr20:30134719-30136176	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr20:30134548-30136326	U87	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:30101906..30104527-chr20:30134975..30136638,2	K562	blood:
2	chr20:30123909..30126939-chr20:30134213..30136284,3	MCF-7	breast:
3	chr20:30133664..30136145-chr20:30192158..30194611,3	MCF-7	breast:
4	chr20:30134823..30136546-chr20:30160807..30162785,2	K562	blood:
5	chr20:30133621..30137235-chr20:30141134..30146018,8	MCF-7	breast:
6	chr20:30132728..30137690-chr20:30191198..30195140,7	K562	blood:
7	chr20:30134774..30136702-chr20:30191198..30194959,4	K562	blood:
8	chr20:30135136..30139255-chr20:30153713..30156690,3	MCF-7	breast:

No data

Variant related genes	Relation type
HM13	TF binding region
ENSG00000101294	Chromatin interaction
ENSG00000230613	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000264395	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2233834	0.91[CEU][hapmap]
rs6057911	0.88[CEU][hapmap]
rs6057912	0.91[CEU][hapmap]
rs717064	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
2	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
3	nsv1062069	chr20:29833958-30153486	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1062612	chr20:29833958-30219337	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
5	nsv1061673	chr20:29833958-30649496	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer 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	422 gene(s)	inside rSNPs	diseases
6	nsv544232	chr20:29833958-30649496	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
7	nsv1058344	chr20:29835037-30386611	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	402 gene(s)	inside rSNPs	diseases
8	nsv1059672	chr20:29835037-30621271	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
9	esv2763228	chr20:29835049-30239522	Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
10	nsv949085	chr20:29846303-30473188	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	414 gene(s)	inside rSNPs	diseases
11	nsv1058020	chr20:29877877-30197681	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
12	nsv544236	chr20:29877877-30197681	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
13	nsv1063560	chr20:29877877-30435888	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
14	nsv544237	chr20:29877877-30435888	Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
15	nsv458961	chr20:29893501-30275906	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
16	nsv585911	chr20:29893501-30275906	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
17	nsv1067177	chr20:29900572-30299363	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
18	nsv1067419	chr20:30029545-30162261	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv544238	chr20:30029545-30162261	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv1057001	chr20:30108573-30190814	Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
21	nsv544239	chr20:30108573-30190814	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1115713	FRG1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:30134200-30136000	Active TSS	Brain Angular Gyrus	brain
2	chr20:30134200-30136000	Active TSS	Fetal Intestine Large	intestine
3	chr20:30134200-30136000	Active TSS	Fetal Lung	lung
4	chr20:30134200-30136200	Active TSS	Fetal Kidney	kidney
5	chr20:30134200-30136400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:30134200-30136400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr20:30134200-30136400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:30134200-30136400	Active TSS	Colonic Mucosa	Colon
9	chr20:30134200-30136800	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr20:30134200-30136800	Transcr. at gene 5' and 3'	HepG2	liver
11	chr20:30134200-30137200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:30134200-30144800	Strong transcription	A549	lung
13	chr20:30134400-30136000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:30134400-30136000	Active TSS	Brain Germinal Matrix	brain
15	chr20:30134400-30136000	Active TSS	Fetal Muscle Trunk	muscle
16	chr20:30134400-30136200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr20:30134400-30136200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr20:30134400-30136200	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr20:30134400-30136200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
20	chr20:30134400-30136200	Active TSS	Rectal Smooth Muscle	rectum
21	chr20:30134400-30136400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr20:30134400-30136400	Active TSS	Psoas Muscle	Psoas
23	chr20:30134400-30136400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
24	chr20:30134400-30136600	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
25	chr20:30134400-30136800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
26	chr20:30134600-30136000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr20:30134600-30136000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr20:30134600-30136000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr20:30134600-30136000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr20:30134600-30136000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr20:30134600-30136000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
32	chr20:30134600-30136000	Active TSS	Brain Cingulate Gyrus	brain
33	chr20:30134600-30136000	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr20:30134600-30136000	Active TSS	Brain Substantia Nigra	brain
35	chr20:30134600-30136000	Active TSS	Colon Smooth Muscle	Colon
36	chr20:30134600-30136000	Active TSS	Ovary	ovary
37	chr20:30134600-30136000	Active TSS	Stomach Mucosa	stomach
38	chr20:30134600-30136000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
39	chr20:30134600-30136200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr20:30134600-30136200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr20:30134600-30136200	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr20:30134600-30136200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
43	chr20:30134600-30136200	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr20:30134600-30136200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
45	chr20:30134600-30136200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr20:30134600-30136400	Active TSS	H1 Cell Line	embryonic stem cell
47	chr20:30134600-30136400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:30134600-30136400	Transcr. at gene 5' and 3'	Liver	Liver
49	chr20:30134600-30136400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr20:30134600-30136600	Transcr. at gene 5' and 3'	NHLF	lung

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