Variant report

Variant	rs4664349
Chromosome Location	chr2:152193359-152193360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152116855..152118703-chr2:152192854..152195590,2	K562	blood:

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1023635	0.89[EUR][1000 genomes]
rs1048135	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11678123	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678951	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680338	0.84[ASN][1000 genomes]
rs11683487	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11691055	0.83[ASN][1000 genomes]
rs11691217	0.83[ASN][1000 genomes]
rs11692626	0.86[EUR][1000 genomes]
rs11730	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12467046	0.84[ASN][1000 genomes]
rs12469634	0.87[MEX][hapmap]
rs12471191	0.83[ASN][1000 genomes]
rs12471886	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12476687	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12624156	0.90[ASN][1000 genomes]
rs12693004	0.90[ASN][1000 genomes]
rs12987765	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12996459	0.84[ASN][1000 genomes]
rs12999396	0.87[EUR][1000 genomes]
rs13001328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004590	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015862	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13018429	0.87[EUR][1000 genomes]
rs13020443	0.86[EUR][1000 genomes]
rs13020962	0.84[ASN][1000 genomes]
rs13025888	0.81[ASN][1000 genomes]
rs13027425	0.84[ASN][1000 genomes]
rs17796622	0.87[MEX][hapmap]
rs17798290	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2113508	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2218880	0.82[ASN][1000 genomes]
rs2271811	0.91[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs2278090	0.89[ASN][1000 genomes]
rs34028108	0.91[ASN][1000 genomes]
rs34408744	0.87[EUR][1000 genomes]
rs34452578	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34538548	0.89[ASN][1000 genomes]
rs35659175	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35723696	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35863408	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771882	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3845843	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3854012	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3856557	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664322	0.88[EUR][1000 genomes]
rs4664336	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664347	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665114	0.84[ASN][1000 genomes]
rs4665137	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4665150	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4665168	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55775354	0.84[ASN][1000 genomes]
rs56335263	0.90[ASN][1000 genomes]
rs56376752	0.83[ASN][1000 genomes]
rs57201382	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433327	0.85[GIH][hapmap]
rs66521733	0.87[ASN][1000 genomes]
rs66588921	0.80[ASN][1000 genomes]
rs6705511	0.86[MEX][hapmap]
rs6707889	0.87[EUR][1000 genomes]
rs6708382	0.84[GIH][hapmap]
rs6713041	0.81[EUR][1000 genomes]
rs6726634	0.85[GIH][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs67303849	0.81[ASN][1000 genomes]
rs6739517	0.82[ASN][1000 genomes]
rs6757821	0.81[CHB][hapmap]
rs67725431	0.90[ASN][1000 genomes]
rs68058019	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73004003	0.89[EUR][1000 genomes]
rs7349449	0.87[EUR][1000 genomes]
rs7558169	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559296	0.82[ASN][1000 genomes]
rs7574228	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287955	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4664349	TNFAIP6	cis	multi-tissue	Pritchard
rs4664349	TNFAIP6	cis	Whole Blood	GTEx
rs4664349	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs4664349	NMI	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152189400-152194800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:152190400-152194200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:152191200-152194000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:152191200-152194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:152191200-152194600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:152191200-152194800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:152191200-152195000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:152191200-152195400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:152191200-152195600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:152191400-152193400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:152191400-152193400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:152191400-152193600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:152191400-152193600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:152191400-152195200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:152191400-152195600	Weak transcription	NH-A	brain
16	chr2:152191400-152195600	Weak transcription	NHLF	lung
17	chr2:152191400-152195600	Weak transcription	Osteobl	bone
18	chr2:152191600-152193400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:152191600-152193400	Weak transcription	NHDF-Ad	bronchial
20	chr2:152191600-152193600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:152191600-152194600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:152192200-152196000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr2:152192400-152193400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:152192400-152193800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:152192400-152194000	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:152193200-152194000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr2:152193200-152196000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:152193200-152196000	Enhancers	HUVEC	blood vessel

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