Variant report

Variant	rs749457
Chromosome Location	chr2:96795944-96795945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96794272..96796392-chr2:96913963..96916568,2	MCF-7	breast:
2	chr2:96794874..96796956-chr2:96797395..96799293,2	K562	blood:
3	chr2:96794822..96796734-chr2:96798992..96801500,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10183151	0.87[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1030864	0.83[EUR][1000 genomes]
rs1168965	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs1168966	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168967	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1168968	0.82[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs1168970	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1168972	0.83[EUR][1000 genomes]
rs1168974	0.82[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs1168975	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1168976	0.82[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs13009727	0.83[EUR][1000 genomes]
rs13019188	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes]
rs1657502	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1724120	0.84[LWK][hapmap]
rs1724121	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1724125	0.81[EUR][1000 genomes]
rs2229169	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2252697	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2301707	0.82[CEU][hapmap]
rs2312955	0.82[CEU][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs2438972	0.82[CEU][hapmap]
rs2576437	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2579519	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs2692894	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[EUR][1000 genomes]
rs2917662	0.81[EUR][1000 genomes]
rs2918916	0.85[EUR][1000 genomes]
rs2969490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2969491	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs3111873	0.81[EUR][1000 genomes]
rs3821051	0.82[CEU][hapmap]
rs4426564	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs4907299	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs749459	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7561198	0.80[EUR][1000 genomes]
rs7604842	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs772175	0.82[CEU][hapmap]
rs772178	0.82[CEU][hapmap]
rs893173	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs749457	FAHD2CP	cis	Muscle Skeletal	GTEx
rs749457	ADRA2B	cis	Thyroid	GTEx
rs749457	GPAT2	cis	Muscle Skeletal	GTEx
rs749457	ADRA2B	cis	Nerve Tibial	GTEx
rs749457	MRPL30	cis	parietal	SCAN
rs749457	FAHD2CP	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96783800-96797200	Weak transcription	Gastric	stomach
2	chr2:96786400-96804200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:96787800-96807800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:96788200-96804400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:96788600-96796800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:96789800-96804400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:96790800-96797400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:96792000-96808000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:96794000-96796600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:96794400-96796000	Weak transcription	GM12878-XiMat	blood
11	chr2:96795000-96798600	Strong transcription	Primary T cells from cord blood	blood
12	chr2:96795200-96796600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:96795200-96798200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:96795400-96796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:96795400-96802200	Strong transcription	Thymus	Thymus
16	chr2:96795600-96796400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:96795600-96797400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:96795800-96797600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:96795800-96803200	Weak transcription	Spleen	Spleen
20	chr2:96795800-96804000	Weak transcription	Fetal Thymus	thymus

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