Variant report

Variant	rs4907299
Chromosome Location	chr2:96780122-96780123
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96766427..96768591-chr2:96778243..96780408,2	K562	blood:
2	chr2:96768848..96771320-chr2:96776985..96780678,4	K562	blood:
3	chr2:96777756..96780230-chr2:96872542..96875164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10183151	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1030864	0.90[EUR][1000 genomes]
rs11680950	0.85[CEU][hapmap]
rs1168965	0.95[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs1168966	0.81[EUR][1000 genomes]
rs1168968	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs1168970	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs1168972	0.90[EUR][1000 genomes]
rs1168974	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs1168975	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs1168976	0.90[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs13019188	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1657502	0.84[ASW][hapmap];0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1724121	0.80[EUR][1000 genomes]
rs1724125	0.88[EUR][1000 genomes]
rs2140938	0.86[EUR][1000 genomes]
rs2229169	0.95[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2252697	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2301707	0.90[CEU][hapmap]
rs2312955	0.90[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs2576437	0.81[EUR][1000 genomes]
rs2579549	0.87[EUR][1000 genomes]
rs2579550	0.88[EUR][1000 genomes]
rs2579552	0.87[EUR][1000 genomes]
rs2692893	0.86[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2692894	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2692934	0.86[EUR][1000 genomes]
rs2692935	0.81[EUR][1000 genomes]
rs2692936	0.87[EUR][1000 genomes]
rs2692937	0.89[EUR][1000 genomes]
rs2917662	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2969490	0.81[EUR][1000 genomes]
rs2969491	0.95[CEU][hapmap];0.95[YRI][hapmap];0.95[EUR][1000 genomes]
rs3111873	0.96[EUR][1000 genomes]
rs3821051	0.90[CEU][hapmap]
rs4426564	0.90[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs749457	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs749459	0.84[ASW][hapmap];0.82[CEU][hapmap]
rs7561198	0.95[EUR][1000 genomes]
rs7604842	0.95[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs772175	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs772178	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs893173	0.84[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv1000049	chr2:96740430-96796312	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
9	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
10	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
16	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
19	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
20	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv2834	chr2:96772925-96785110	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
22	nsv874678	chr2:96777340-96786411	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4907299	FAHD2CP	cis	lung	GTEx
rs4907299	ADRA2B	cis	Thyroid	GTEx
rs4907299	FAHD2CP	cis	Muscle Skeletal	GTEx
rs4907299	ZNF514	cis	parietal	SCAN
rs4907299	GPAT2	cis	Muscle Skeletal	GTEx
rs4907299	MGAT4A	cis	parietal	SCAN
rs4907299	MRPL30	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96772000-96782200	Weak transcription	Liver	Liver
2	chr2:96775000-96781800	Weak transcription	Right Atrium	heart
3	chr2:96775400-96780400	Weak transcription	Spleen	Spleen
4	chr2:96775400-96780800	Weak transcription	Lung	lung
5	chr2:96775600-96780400	Weak transcription	Left Ventricle	heart
6	chr2:96775600-96781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:96776200-96780400	Weak transcription	Right Ventricle	heart
8	chr2:96777200-96781400	Weak transcription	Esophagus	oesophagus
9	chr2:96778000-96781000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:96778600-96781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:96779400-96780800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr2:96779600-96780200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:96779800-96780400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:96779800-96781000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:96779800-96781800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
16	chr2:96780000-96780400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr2:96780000-96780800	Enhancers	Brain Cingulate Gyrus	brain

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