Variant report

Variant	rs4849056
Chromosome Location	chr2:112966509-112966510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112961755..112963259-chr2:112964088..112966680,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10169159	0.87[ASN][1000 genomes]
rs10175234	0.83[ASN][1000 genomes]
rs10177573	0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10183121	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10191002	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10196933	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10205038	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10211300	0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10864903	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs11123131	0.85[ASN][1000 genomes]
rs11123132	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11674953	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11688418	0.88[ASN][1000 genomes]
rs11689487	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11691431	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11691794	0.88[ASN][1000 genomes]
rs11903741	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs12620553	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12711737	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12711738	0.94[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12711739	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs13387611	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs13407329	0.85[ASN][1000 genomes]
rs34623958	0.87[ASN][1000 genomes]
rs4299347	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4352239	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4392265	0.87[ASN][1000 genomes]
rs4399734	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4430968	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4446076	0.87[ASN][1000 genomes]
rs4450606	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4456711	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4507112	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4522611	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4525706	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4542853	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4578863	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4622729	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4849057	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542045	0.94[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6542048	0.86[ASN][1000 genomes]
rs6542050	0.87[ASN][1000 genomes]
rs6542051	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6706874	0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713344	1.00[LWK][hapmap]
rs6716010	0.86[ASN][1000 genomes]
rs6733138	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6745942	0.87[ASN][1000 genomes]
rs6751146	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6758110	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6761599	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs72831684	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7557281	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7557862	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs7571435	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7591439	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7598168	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7600338	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7601200	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7601888	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4849056	FBLN7	cis	parietal	SCAN
rs4849056	POLR1B	cis	cerebellum	SCAN
rs4849056	LOC653596	cis	multi-tissue	Pritchard
rs4849056	TMEM87B	cis	parietal	SCAN
rs4849056	MERTK	cis	multi-tissue	Pritchard
rs4849056	FBLN7	cis	cerebellum	SCAN
rs4849056	POLR1B	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
3	chr2:112959200-112969600	Weak transcription	Fetal Thymus	thymus
4	chr2:112959600-112987000	Weak transcription	Osteobl	bone
5	chr2:112961000-112968800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:112962400-112969000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:112962400-112969400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:112962400-112969800	Weak transcription	Liver	Liver
10	chr2:112962400-112979000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:112963200-112966600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:112963200-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:112964000-112973600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:112964800-112969600	Weak transcription	Fetal Brain Female	brain
15	chr2:112964800-112970400	Weak transcription	Dnd41	blood
16	chr2:112965000-112969400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:112965200-112972200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:112965400-112967200	Weak transcription	Aorta	Aorta
19	chr2:112965400-112969800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:112965600-112969600	Weak transcription	Thymus	Thymus
21	chr2:112965600-112971600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:112965600-112972200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:112965800-112969200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:112965800-112969600	Weak transcription	Brain Germinal Matrix	brain
25	chr2:112965800-112971800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:112965800-112972000	Weak transcription	Lung	lung
27	chr2:112965800-112972200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:112966000-112968200	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:112966000-112969800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:112966200-112969600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:112966200-112969600	Weak transcription	Ovary	ovary

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