Variant report

Variant	rs17410308
Chromosome Location	chr1:46078191-46078192
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46077692-46080112	PANC-1	pancreas:	n/a	n/a
2	NR2F2	chr1:46077630-46078260	K562	blood:	n/a	n/a
3	POLR2A	chr1:46078051-46078374	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:46077183-46078754	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:46077960-46079316	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:46077270-46079390	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:46077322-46080261	A549	lung:	n/a	n/a
8	POLR2A	chr1:46077748-46079731	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:46075118-46080217	GM12892	blood:	n/a	n/a
10	PML	chr1:46077303-46079636	K562	blood:	n/a	n/a
11	POLR2A	chr1:46077739-46079690	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:46077704-46078343	K562	blood:	n/a	n/a
13	POLR2A	chr1:46078159-46078767	K562	blood:	n/a	n/a
14	POLR2A	chr1:46077708-46079614	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:46077865-46079198	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:46078154-46079605	GM12891	blood:	n/a	n/a
17	BCL3	chr1:46077331-46079649	K562	blood:	n/a	n/a
18	POLR2A	chr1:46078164-46078435	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:46078034-46079310	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:46077234-46080256	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:46077819-46080258	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:46077808-46078784	K562	blood:	n/a	n/a
23	POLR2A	chr1:46078060-46078363	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:46078179-46078443	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:46077534-46080171	K562	blood:	n/a	n/a
26	TEAD4	chr1:46077746-46079033	K562	blood:	n/a	n/a
27	POLR2A	chr1:46078025-46079521	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46047578..46050794-chr1:46077080..46080053,4	K562	blood:
2	chr1:46077501..46079157-chr1:46087359..46089713,2	K562	blood:
3	chr1:46077123..46079001-chr1:46087359..46089282,2	K562	blood:
4	chr1:46078095..46080443-chr1:46125224..46127311,2	K562	blood:
5	chr1:46076644..46079333-chr1:46150802..46152314,2	K562	blood:
6	chr1:46058928..46062308-chr1:46076785..46078663,3	K562	blood:

No data

Variant related genes	Relation type
NASP	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159588	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12130818	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs487174	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17410308	HYI	cis	cerebellum	SCAN
rs17410308	Hs.396207	cis	multi-tissue	Pritchard
rs17410308	NSUN4	cis	cerebellum	SCAN
rs17410308	FAM183A	cis	parietal	SCAN
rs17410308	IPP	trans	brain	seeQTL
rs17410308	IPP	cis	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052000-46081000	Weak transcription	Small Intestine	intestine
2	chr1:46052200-46084200	Weak transcription	Right Atrium	heart
3	chr1:46052400-46080600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:46052800-46078400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:46052800-46081000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:46052800-46086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46052800-46089200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:46053600-46086000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:46055000-46085200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:46055200-46090400	Strong transcription	Dnd41	blood
13	chr1:46056000-46079000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:46057400-46081600	Weak transcription	Psoas Muscle	Psoas
15	chr1:46061000-46078800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:46066800-46084400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:46066800-46086800	Strong transcription	K562	blood
18	chr1:46067000-46086400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:46067200-46086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:46067200-46087400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:46067400-46086600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:46068000-46078800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:46068000-46086600	Strong transcription	Placenta	Placenta
24	chr1:46068200-46085000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:46068200-46086600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:46068200-46087000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:46068200-46087400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr1:46068200-46087400	Strong transcription	Fetal Thymus	thymus
29	chr1:46068800-46078600	Weak transcription	NHLF	lung
30	chr1:46068800-46080800	Weak transcription	NHDF-Ad	bronchial
31	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:46070800-46080800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:46071000-46087400	Strong transcription	Fetal Stomach	stomach
34	chr1:46071200-46093000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:46071600-46087200	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:46072000-46084200	Strong transcription	Hela-S3	cervix
38	chr1:46072200-46084400	Strong transcription	Fetal Lung	lung
39	chr1:46073200-46079200	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:46073600-46079400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:46073800-46078200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:46073800-46079000	Weak transcription	Ovary	ovary
43	chr1:46074000-46079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:46074200-46080000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:46074400-46082000	Weak transcription	Fetal Brain Male	brain
46	chr1:46074600-46078200	Weak transcription	Brain Germinal Matrix	brain
47	chr1:46074600-46078600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:46074600-46078800	Weak transcription	Spleen	Spleen
49	chr1:46074600-46079400	Weak transcription	Brain Substantia Nigra	brain
50	chr1:46074600-46080600	Weak transcription	Pancreas	Pancrea

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