Variant report

Variant	rs2580766
Chromosome Location	chr2:55204800-55204801
allele	C/G
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	MTA3	chr2:55204209-55204803	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:55204478-55205270	HUVEC	blood vessel:	n/a	n/a
3	BCLAF1	chr2:55204196-55204809	GM12878	blood:	n/a	chr2:55204561-55204570
4	MEF2A	chr2:55204295-55204811	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:55204536-55204858	SK-N-SH	brain:	n/a	n/a
6	MEF2C	chr2:55204224-55204807	GM12878	blood:	n/a	chr2:55204519-55204534
7	POLR2A	chr2:55201696-55205299	K562	blood:	n/a	n/a
8	ZNF384	chr2:55204223-55204819	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55204435..55209089-chr2:55274911..55278052,4	MCF-7	breast:
2	chr2:55180338..55182211-chr2:55203492..55207061,3	MCF-7	breast:
3	chr2:55197790..55202065-chr2:55203128..55206918,7	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10179594	0.82[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs10196667	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10198636	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10205017	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746530	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11125551	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12989576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13002841	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13023202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13026576	1.00[AFR][1000 genomes]
rs17418111	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2580763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920839	0.91[EUR][1000 genomes]
rs2920863	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920883	0.82[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs2920884	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2920889	0.82[EUR][1000 genomes]
rs2920890	0.82[EUR][1000 genomes]
rs2920897	0.82[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2920898	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2968789	0.82[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2968812	0.84[JPT][hapmap]
rs2968813	0.85[JPT][hapmap]
rs2968814	0.85[JPT][hapmap]
rs2968823	0.82[EUR][1000 genomes]
rs2968824	0.82[EUR][1000 genomes]
rs2968826	0.84[EUR][1000 genomes]
rs2968831	0.90[EUR][1000 genomes]
rs2972066	0.82[EUR][1000 genomes]
rs2972069	0.82[EUR][1000 genomes]
rs2972076	0.91[EUR][1000 genomes]
rs34227740	1.00[AFR][1000 genomes]
rs34564860	1.00[AFR][1000 genomes]
rs36024305	1.00[AFR][1000 genomes]
rs4671233	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4671998	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55777421	1.00[AFR][1000 genomes]
rs6545462	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs67721747	1.00[AFR][1000 genomes]
rs7559248	1.00[AFR][1000 genomes];0.89[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2580766	RTN4	cis	Thyroid	GTEx

Chromatin state (count:143 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
2	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:55193400-55214800	Strong transcription	HepG2	liver
6	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:55195000-55215200	Strong transcription	Dnd41	blood
10	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:55195200-55205800	Strong transcription	HMEC	breast
12	chr2:55195400-55205200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:55196000-55205800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
18	chr2:55196600-55208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55196800-55204800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:55196800-55205600	Strong transcription	NHEK	skin
23	chr2:55197200-55204800	Strong transcription	K562	blood
24	chr2:55197800-55207800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:55198600-55215200	Weak transcription	Lung	lung
28	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:55199000-55206800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:55199200-55206600	Weak transcription	Hela-S3	cervix
31	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:55199400-55208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:55199600-55204800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:55200200-55209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
36	chr2:55200800-55208000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
38	chr2:55201000-55208400	Weak transcription	Placenta	Placenta
39	chr2:55201200-55205200	Genic enhancers	HSMM	muscle
40	chr2:55201200-55208000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:55201400-55208400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:55201800-55204800	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr2:55201800-55205000	Enhancers	Brain Hippocampus Middle	brain
44	chr2:55202000-55204800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:55202000-55207800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:55202200-55204800	Enhancers	Adipose Nuclei	Adipose
47	chr2:55202200-55204800	Enhancers	Colon Smooth Muscle	Colon
48	chr2:55202200-55205000	Enhancers	Brain Angular Gyrus	brain
49	chr2:55202200-55205000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr2:55202200-55205200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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