Variant report

Variant	rs7584187
Chromosome Location	chr2:172866105-172866106
allele	A/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	GTF2F1	chr2:172865887-172866145	K562	blood:	n/a	n/a
2	POLR2A	chr2:172864483-172866178	K562	blood:	n/a	n/a
3	MYC	chr2:172864384-172866113	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
4	ZNF384	chr2:172864695-172866150	K562	blood:	n/a	n/a
5	MYC	chr2:172864384-172866232	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
6	STAT3	chr2:172866057-172866126	MCF10A-Er-Src	breast:	n/a	n/a
7	JUN	chr2:172864128-172866370	K562	blood:	n/a	chr2:172864832-172864841
8	MAX	chr2:172864419-172866140	NB4	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
9	TBP	chr2:172864332-172866122	K562	blood:	n/a	n/a
10	MYC	chr2:172864469-172866119	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
11	POLR2A	chr2:172865632-172866105	K562	blood:	n/a	n/a
12	JUND	chr2:172865841-172866214	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172864878..172867088-chr2:172885343..172888601,3	MCF-7	breast:
2	chr2:172836942..172840182-chr2:172865086..172867545,3	K562	blood:
3	chr2:172866012..172868252-chr2:172888365..172889925,2	K562	blood:
4	chr2:172865192..172866696-chr2:172882365..172884619,2	K562	blood:
5	chr2:172860607..172867322-chr2:172946572..172954768,24	MCF-7	breast:
6	chr2:172863189..172867097-chr2:172945137..172953576,15	K562	blood:
7	chr2:172777448..172780536-chr2:172864307..172867165,5	K562	blood:
8	chr2:172777448..172780686-chr2:172863264..172866650,5	K562	blood:
9	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
10	chr2:172861569..172867068-chr2:172965912..172971063,13	K562	blood:
11	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
12	chr2:172865319..172867165-chr2:172958797..172961537,3	MCF-7	breast:
13	chr2:172289221..172292184-chr2:172864925..172866500,2	K562	blood:
14	chr2:172377500..172380432-chr2:172864656..172866178,2	K562	blood:
15	chr2:172837275..172840182-chr2:172865086..172867056,2	K562	blood:
16	chr11:65265208..65268065-chr2:172864519..172866349,2	MCF-7	breast:
17	chr2:172862808..172868920-chr2:172961807..172971063,13	K562	blood:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000123600	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000128708	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1008151	0.84[CHB][hapmap]
rs11675404	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11676438	0.84[AMR][1000 genomes]
rs12052246	0.89[CEU][hapmap]
rs12987931	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs12991740	0.89[CEU][hapmap]
rs13020884	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs1965160	0.92[CHB][hapmap]
rs1996424	0.81[JPT][hapmap]
rs2271758	0.83[CEU][hapmap]
rs4581870	0.85[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs55653103	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182436	0.85[AMR][1000 genomes]
rs62183769	0.87[AMR][1000 genomes]
rs62183770	0.87[AMR][1000 genomes]
rs62183782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183783	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183800	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183801	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433323	0.89[CEU][hapmap]
rs6718013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729945	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6730085	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733794	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737308	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6746701	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7557612	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598246	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7584187	MAP1D	cis	cerebellum	SCAN
rs7584187	DYNC1I2	cis	cerebellum	SCAN
rs7584187	MAP1D	cis	parietal	SCAN
rs7584187	AC068039.4	cis	Muscle Skeletal	GTEx
rs7584187	AC068039.4	cis	Thyroid	GTEx
rs7584187	SLC25A12	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172864400-172866200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr2:172865000-172866200	Flanking Active TSS	Dnd41	blood
3	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:172865400-172877200	Weak transcription	Pancreas	Pancrea
5	chr2:172865400-172878000	Weak transcription	Gastric	stomach
6	chr2:172865600-172866200	Enhancers	Liver	Liver
7	chr2:172865600-172866200	Enhancers	HMEC	breast
8	chr2:172865600-172869600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:172865600-172870400	Weak transcription	Right Ventricle	heart
10	chr2:172865600-172875200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:172865600-172876600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:172865600-172877200	Weak transcription	Psoas Muscle	Psoas
13	chr2:172865600-172878000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
15	chr2:172865800-172866200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:172865800-172866200	Enhancers	Hela-S3	cervix
17	chr2:172865800-172866200	Flanking Active TSS	K562	blood
18	chr2:172865800-172866400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:172865800-172867400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:172865800-172869000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:172865800-172869800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:172865800-172876600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:172865800-172877200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:172865800-172877600	Weak transcription	Fetal Kidney	kidney
25	chr2:172865800-172878000	Weak transcription	Primary B cells from cord blood	blood
26	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:172866000-172866200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:172866000-172866200	Enhancers	HepG2	liver
30	chr2:172866000-172868800	Weak transcription	Stomach Mucosa	stomach
31	chr2:172866000-172872600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:172866000-172873600	Weak transcription	Fetal Lung	lung
33	chr2:172866000-172876400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:172866000-172877200	Weak transcription	Ovary	ovary
35	chr2:172866000-172877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:172866000-172877800	Weak transcription	HSMM	muscle
37	chr2:172866000-172878000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle

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