Variant report

Variant	rs829958
Chromosome Location	chr2:169658783-169658784
allele	C/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	SP1	chr2:169658728-169659377	A549	lung:	n/a	n/a
2	MAX	chr2:169658723-169659281	K562	blood:	n/a	n/a
3	JUND	chr2:169658619-169660226	K562	blood:	n/a	chr2:169659930-169659939 chr2:169660049-169660058 chr2:169660017-169660029
4	TEAD4	chr2:169658489-169660182	K562	blood:	n/a	n/a
5	NR2F2	chr2:169658480-169659319	K562	blood:	n/a	n/a
6	ZNF143	chr2:169658724-169659342	K562	blood:	n/a	n/a
7	ZC3H11A	chr2:169658673-169659352	K562	blood:	n/a	n/a
8	STAT5A	chr2:169658757-169659599	K562	blood:	n/a	chr2:169659358-169659372 chr2:169659014-169659021
9	GTF2B	chr2:169658783-169659292	K562	blood:	n/a	n/a
10	POLR2A	chr2:169658621-169659412	K562	blood:	n/a	n/a
11	SP1	chr2:169658712-169659327	A549	lung:	n/a	n/a
12	FOXA2	chr2:169658725-169659266	A549	lung:	n/a	n/a
13	TBL1XR1	chr2:169658734-169660303	K562	blood:	n/a	n/a
14	ATF1	chr2:169658557-169660150	K562	blood:	n/a	n/a
15	ZMIZ1	chr2:169658719-169659397	K562	blood:	n/a	n/a
16	NR3C1	chr2:169658759-169659291	A549	lung:	n/a	n/a
17	ELF1	chr2:169658718-169659406	HCT-116	colon:	n/a	chr2:169659067-169659076 chr2:169659066-169659077 chr2:169659066-169659077
18	POLR2A	chr2:169658783-169659324	K562	blood:	n/a	n/a
19	ELF1	chr2:169658725-169659402	MCF-7	breast:	n/a	chr2:169659067-169659076 chr2:169659066-169659077 chr2:169659066-169659077
20	RCOR1	chr2:169658656-169660156	K562	blood:	n/a	n/a
21	CBX3	chr2:169658410-169660111	K562	blood:	n/a	n/a
22	TEAD4	chr2:169658737-169660249	K562	blood:	n/a	n/a
23	ELF1	chr2:169658765-169659308	A549	lung:	n/a	chr2:169659067-169659076 chr2:169659066-169659077 chr2:169659066-169659077
24	MAZ	chr2:169658615-169660110	K562	blood:	n/a	n/a
25	TRIM28	chr2:169658583-169660198	K562	blood:	n/a	chr2:169658864-169658872
26	TBP	chr2:169658610-169660163	K562	blood:	n/a	n/a
27	NR3C1	chr2:169658757-169659314	A549	lung:	n/a	n/a
28	MYC	chr2:169658575-169660211	K562	blood:	n/a	n/a
29	MYC	chr2:169658630-169661078	K562	blood:	n/a	chr2:169660713-169660722
30	NR2F2	chr2:169658066-169660165	K562	blood:	n/a	n/a
31	ELK1	chr2:169658647-169659257	K562	blood:	n/a	n/a
32	TCF12	chr2:169658669-169659561	A549	lung:	n/a	n/a
33	ELF1	chr2:169658663-169659240	K562	blood:	n/a	chr2:169659067-169659076 chr2:169659066-169659077 chr2:169659066-169659077
34	TAF1	chr2:169658777-169659301	K562	blood:	n/a	n/a
35	MAFK	chr2:169658672-169659304	K562	blood:	n/a	n/a
36	HEY1	chr2:169658696-169659339	K562	blood:	n/a	n/a
37	ELF1	chr2:169658636-169659446	HCT-116	colon:	n/a	chr2:169659067-169659076 chr2:169659066-169659077 chr2:169659066-169659077
38	UBTF	chr2:169658648-169659254	K562	blood:	n/a	n/a
39	PML	chr2:169658772-169660178	K562	blood:	n/a	chr2:169658864-169658872
40	EP300	chr2:169658782-169660250	K562	blood:	n/a	chr2:169659015-169659024 chr2:169659854-169659864 chr2:169659069-169659076 chr2:169660051-169660060
41	JUN	chr2:169657816-169661502	K562	blood:	n/a	chr2:169659930-169659939 chr2:169660049-169660058 chr2:169658084-169658096 chr2:169660017-169660029 chr2:169658085-169658095
42	POLR2A	chr2:169658766-169659345	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:169658771-169659524	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:169658744-169659829	K562	blood:	n/a	n/a

Variant related genes	Relation type
NOSTRIN	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16855794	1.00[CHD][hapmap]
rs17200279	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs514629	0.90[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[EUR][1000 genomes]
rs7583629	0.90[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[EUR][1000 genomes]
rs829957	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829958	CXCL14	trans	lymphoblastoid	seeQTL
rs829958	SCN7A	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169652000-169659000	Weak transcription	Fetal Kidney	kidney
2	chr2:169652200-169658800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:169653000-169658800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:169653000-169658800	Weak transcription	Ovary	ovary
5	chr2:169653000-169659000	Weak transcription	Right Ventricle	heart
6	chr2:169653000-169659200	Enhancers	Fetal Intestine Small	intestine
7	chr2:169655400-169658800	Weak transcription	Fetal Lung	lung
8	chr2:169656000-169666800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:169656200-169658800	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:169656200-169658800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:169656200-169659000	Weak transcription	Spleen	Spleen
12	chr2:169656600-169659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:169656600-169659400	Weak transcription	Gastric	stomach
14	chr2:169656800-169658800	Weak transcription	Left Ventricle	heart
15	chr2:169657800-169659200	Enhancers	Fetal Intestine Large	intestine
16	chr2:169658000-169658800	Enhancers	Lung	lung
17	chr2:169658000-169658800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:169658000-169658800	Enhancers	Hela-S3	cervix
19	chr2:169658000-169659000	Enhancers	Colonic Mucosa	Colon
20	chr2:169658200-169659000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:169658200-169659000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:169658200-169659200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:169658200-169659200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:169658200-169659200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:169658200-169659200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:169658200-169659200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr2:169658200-169659200	Enhancers	Fetal Heart	heart
28	chr2:169658200-169659400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr2:169658200-169659800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:169658400-169658800	Enhancers	Adipose Nuclei	Adipose
31	chr2:169658400-169658800	Enhancers	Small Intestine	intestine
32	chr2:169658400-169658800	Enhancers	Stomach Mucosa	stomach
33	chr2:169658400-169659000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:169658400-169659000	Enhancers	Fetal Stomach	stomach
35	chr2:169658400-169659200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr2:169658400-169659400	Enhancers	Placenta	Placenta
37	chr2:169658400-169659800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr2:169658400-169659800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr2:169658400-169659800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr2:169658400-169660000	Enhancers	HepG2	liver
41	chr2:169658400-169660400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:169658600-169658800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:169658600-169658800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:169658600-169658800	Enhancers	Pancreas	Pancrea
45	chr2:169658600-169659000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr2:169658600-169659200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:169658600-169659200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr2:169658600-169659600	Enhancers	HUVEC	blood vessel
49	chr2:169658600-169659800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:169658600-169659800	Flanking Active TSS	K562	blood

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