Variant report

Variant	rs3733260
Chromosome Location	chr4:129208259-129208260
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	CHD1	chr4:129207540-129208436	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr4:129207599-129208320	A549	lung:	n/a	n/a
3	POLR2A	chr4:129207711-129210246	GM18951	blood:	n/a	n/a
4	POLR2A	chr4:129208257-129209907	K562	blood:	n/a	n/a
5	UBTF	chr4:129207914-129210111	K562	blood:	n/a	n/a
6	POLR2A	chr4:129207453-129210280	HepG2	liver:	n/a	n/a
7	ZBTB7A	chr4:129208237-129208633	K562	blood:	n/a	n/a
8	YY1	chr4:129208216-129209854	HepG2	liver:	n/a	chr4:129209050-129209059 chr4:129208394-129208405 chr4:129209478-129209492 chr4:129209478-129209487 chr4:129209476-129209487 chr4:129209475-129209489 chr4:129208974-129208983
9	POLR2A	chr4:129208149-129210282	ProgFib	skin:	n/a	n/a
10	POLR2A	chr4:129208209-129210338	K562	blood:	n/a	n/a
11	NR2F2	chr4:129207583-129208374	K562	blood:	n/a	n/a
12	SMARCB1	chr4:129207867-129209820	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr4:129207095-129210225	IMR90	lung:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
14	MAX	chr4:129208242-129210429	HepG2	liver:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
15	ZNF384	chr4:129207500-129208276	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:129208197-129209901	GM19193	blood:	n/a	n/a
17	POLR2A	chr4:129207393-129208309	MCF10A-Er-Src	breast:	n/a	n/a
18	MTA3	chr4:129207675-129208303	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr4:129208247-129208624	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr4:129208229-129208676	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:129207173-129211125	IMR90	lung:	n/a	n/a
22	SIN3A	chr4:129207494-129210278	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr4:129208235-129210026	A549	lung:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
24	POLR2A	chr4:129207094-129208293	K562	blood:	n/a	n/a
25	POLR2A	chr4:129208151-129209891	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:129207684-129210259	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr4:129208248-129208677	A549	lung:	n/a	n/a
28	POLR2A	chr4:129208246-129208675	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr4:129208190-129208691	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr4:129207776-129210388	IMR90	lung:	n/a	n/a
31	POLR2A	chr4:129207557-129210389	GM12878	blood:	n/a	n/a
32	ELF1	chr4:129208198-129209963	GM12878	blood:	n/a	chr4:129209001-129209013
33	HMGN3	chr4:129208252-129209871	K562	blood:	n/a	n/a
34	POLR2A	chr4:129207552-129210483	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr4:129208247-129208670	A549	lung:	n/a	n/a
36	POLR2A	chr4:129208253-129208690	GM12878	blood:	n/a	n/a
37	TBP	chr4:129208238-129209759	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr4:129208119-129209936	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr4:129207639-129210352	A549	lung:	n/a	chr4:129209048-129209058 chr4:129209152-129209162 chr4:129209110-129209120
40	MXI1	chr4:129206440-129210496	SK-N-SH	brain:	n/a	chr4:129209521-129209530
41	RAD21	chr4:129207512-129210242	IMR90	lung:	n/a	chr4:129208976-129208986 chr4:129209747-129209761
42	JUND	chr4:129208168-129208510	A549	lung:	n/a	n/a
43	ZNF384	chr4:129207273-129208411	K562	blood:	n/a	n/a
44	POLR2A	chr4:129206953-129209782	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr4:129206571-129210217	IMR90	lung:	n/a	chr4:129209521-129209530

No.	Distal block	Cell Line	Cell type
1	chr4:129207739..129209319-chr4:129473480..129475503,2	MCF-7	breast:
2	chr4:129206178..129209498-chr4:129731212..129733921,5	K562	blood:
3	chr4:128981725..128985397-chr4:129207989..129209697,3	K562	blood:
4	chr4:128981698..128985397-chr4:129207989..129210555,4	K562	blood:
5	chr4:128980817..128984026-chr4:129207052..129210590,3	MCF-7	breast:
6	chr4:129191253..129196346-chr4:129207111..129210585,6	MCF-7	breast:
7	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
8	chr4:129207558..129209105-chr4:129728853..129730896,2	K562	blood:

Variant related genes	Relation type
PGRMC2	TF binding region
ENSG00000164040	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10001857	0.95[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs12509379	0.94[EUR][1000 genomes]
rs12647536	0.95[EUR][1000 genomes]
rs3796500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41300367	0.95[EUR][1000 genomes]
rs4834232	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4975198	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4975221	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs6840580	1.00[LWK][hapmap]
rs7677888	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7680523	0.95[EUR][1000 genomes]
rs7681053	0.94[EUR][1000 genomes]
rs7681074	0.92[EUR][1000 genomes]
rs7682168	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9683654	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv3421519	chr4:129208027-129210875	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3733260	DYNC2LI1	trans	cerebellum	SCAN
rs3733260	HSPA4L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129204800-129210800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:129205200-129210000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:129205400-129208600	Active TSS	Stomach Mucosa	stomach
4	chr4:129205400-129209800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:129205600-129210400	Active TSS	Fetal Intestine Small	intestine
6	chr4:129205600-129210600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:129205800-129209800	Active TSS	Duodenum Mucosa	Duodenum
8	chr4:129205800-129210000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:129205800-129210200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:129205800-129210200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr4:129205800-129210600	Active TSS	Fetal Brain Female	brain
12	chr4:129206000-129209200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:129206000-129209800	Active TSS	HSMMtube	muscle
14	chr4:129206000-129210000	Active TSS	Fetal Stomach	stomach
15	chr4:129206000-129210000	Active TSS	NHLF	lung
16	chr4:129206000-129210200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr4:129206000-129210200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:129206000-129210400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:129206000-129210400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr4:129206000-129210400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:129206000-129210400	Active TSS	Fetal Intestine Large	intestine
22	chr4:129206000-129210400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr4:129206000-129210600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:129206000-129210600	Active TSS	A549	lung
25	chr4:129206200-129208400	Active TSS	Right Atrium	heart
26	chr4:129206200-129209800	Active TSS	Rectal Smooth Muscle	rectum
27	chr4:129206200-129209800	Active TSS	Hela-S3	cervix
28	chr4:129206200-129209800	Active TSS	HSMM	muscle
29	chr4:129206200-129210200	Active TSS	Colonic Mucosa	Colon
30	chr4:129206200-129210400	Active TSS	Right Ventricle	heart
31	chr4:129206400-129209800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr4:129206400-129210000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:129206400-129210000	Active TSS	NHDF-Ad	bronchial
34	chr4:129206400-129210200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:129206400-129210400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:129206600-129209600	Active TSS	Placenta	Placenta
37	chr4:129206600-129210000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr4:129206600-129210200	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:129206800-129208400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr4:129206800-129209600	Active TSS	HMEC	breast
41	chr4:129206800-129209800	Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:129206800-129210000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:129206800-129210000	Active TSS	Brain Germinal Matrix	brain
44	chr4:129206800-129210200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:129206800-129210200	Active TSS	Ovary	ovary
46	chr4:129206800-129210400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:129206800-129211000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:129207000-129208400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr4:129207000-129208600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr4:129207000-129208600	Active TSS	Fetal Brain Male	brain

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