Variant report

Variant	rs55775354
Chromosome Location	chr2:152118271-152118272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152117804..152120182-chr2:152144785..152147621,2	MCF-7	breast:
2	chr2:152115426..152120009-chr2:152142898..152146726,5	K562	blood:
3	chr2:152116994..152118893-chr2:152266218..152268136,2	MCF-7	breast:
4	chr2:152116678..152120470-chr2:152265032..152268454,8	MCF-7	breast:
5	chr2:152116022..152119511-chr2:152263980..152267786,5	K562	blood:
6	chr2:152117446..152118302-chr8:97247298..97247872,2	HCT-116	colon:
7	chr2:152116868..152120610-chr2:152144685..152147660,4	MCF-7	breast:
8	chr2:152117778..152118631-chr7:26240204..26240803,2	NB4	blood:
9	chr2:152117973..152120026-chr2:152143620..152147532,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction
ENSG00000123609	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000254224	Chromatin interaction
ENSG00000156467	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10165186	0.80[EUR][1000 genomes]
rs10165284	0.80[EUR][1000 genomes]
rs10184314	0.81[EUR][1000 genomes]
rs10201139	0.80[EUR][1000 genomes]
rs10203366	0.81[EUR][1000 genomes]
rs10207408	0.80[EUR][1000 genomes]
rs10209942	0.80[EUR][1000 genomes]
rs10210155	0.80[EUR][1000 genomes]
rs1048135	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678123	0.84[ASN][1000 genomes]
rs11680338	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683487	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11691055	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11691217	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471191	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476687	0.83[ASN][1000 genomes]
rs12624156	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693004	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987765	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996459	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998170	0.81[EUR][1000 genomes]
rs13001328	0.84[ASN][1000 genomes]
rs13004590	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13007728	0.82[EUR][1000 genomes]
rs13015862	0.81[ASN][1000 genomes]
rs13020769	0.81[EUR][1000 genomes]
rs13020962	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025888	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027425	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030194	0.81[EUR][1000 genomes]
rs13412131	0.81[EUR][1000 genomes]
rs13420739	0.81[EUR][1000 genomes]
rs17798290	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113508	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2194492	0.81[EUR][1000 genomes]
rs2218880	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271811	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278090	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880488	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs289904	0.86[EUR][1000 genomes]
rs289905	0.86[EUR][1000 genomes]
rs289906	0.89[EUR][1000 genomes]
rs289907	0.86[EUR][1000 genomes]
rs289921	0.85[EUR][1000 genomes]
rs289923	0.89[EUR][1000 genomes]
rs289924	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34028108	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34092307	0.81[EUR][1000 genomes]
rs34385951	0.80[EUR][1000 genomes]
rs34452578	0.86[ASN][1000 genomes]
rs34538548	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34639984	0.80[EUR][1000 genomes]
rs35371567	0.81[EUR][1000 genomes]
rs35613168	0.81[EUR][1000 genomes]
rs35659175	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35723696	0.84[ASN][1000 genomes]
rs35791982	0.81[EUR][1000 genomes]
rs35863408	0.84[ASN][1000 genomes]
rs3771882	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3854012	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856557	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664319	0.83[EUR][1000 genomes]
rs4664320	0.81[EUR][1000 genomes]
rs4664336	0.84[ASN][1000 genomes]
rs4664347	0.84[ASN][1000 genomes]
rs4664349	0.84[ASN][1000 genomes]
rs4665051	0.87[AFR][1000 genomes]
rs4665114	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665137	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665150	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4665163	0.81[EUR][1000 genomes]
rs4665168	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4665169	0.81[EUR][1000 genomes]
rs56335263	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56376752	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57201382	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59247111	0.81[EUR][1000 genomes]
rs6433325	0.81[EUR][1000 genomes]
rs6433327	0.81[EUR][1000 genomes]
rs66521733	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66588921	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705180	0.81[EUR][1000 genomes]
rs6708382	0.81[EUR][1000 genomes]
rs6713041	0.81[EUR][1000 genomes]
rs67181317	0.80[EUR][1000 genomes]
rs67303849	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752471	0.82[EUR][1000 genomes]
rs67693192	0.81[EUR][1000 genomes]
rs67725431	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67868855	0.81[EUR][1000 genomes]
rs7558169	0.84[ASN][1000 genomes]
rs7559296	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7574228	0.84[ASN][1000 genomes]
rs7587037	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9287955	0.81[EUR][1000 genomes]
rs9287956	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1014936	chr2:152019809-152118479	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55775354	TNFAIP6	cis	Muscle Skeletal	GTEx
rs55775354	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs55775354	RBM43	cis	Whole Blood	GTEx
rs55775354	TNFAIP6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152116800-152118600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:152116800-152118600	Active TSS	Rectal Smooth Muscle	rectum
3	chr2:152116800-152118800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:152116800-152118800	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:152117000-152118400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:152117000-152118400	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr2:152117000-152118600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:152117000-152118600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:152117000-152118600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:152117000-152118600	Active TSS	Fetal Lung	lung
11	chr2:152117000-152118600	Active TSS	Fetal Muscle Leg	muscle
12	chr2:152117000-152118600	Active TSS	Fetal Stomach	stomach
13	chr2:152117000-152118600	Active TSS	A549	lung
14	chr2:152117000-152118600	Active TSS	NHDF-Ad	bronchial
15	chr2:152117000-152118600	Active TSS	NHLF	lung
16	chr2:152117000-152118800	Active TSS	Colon Smooth Muscle	Colon
17	chr2:152117000-152119000	Active TSS	Brain Anterior Caudate	brain
18	chr2:152117200-152118400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr2:152117200-152118400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:152117200-152118400	Active TSS	HSMMtube	muscle
21	chr2:152117200-152118600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:152117200-152118600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:152117200-152118600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr2:152117200-152118600	Active TSS	Fetal Kidney	kidney
25	chr2:152117200-152118600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr2:152117200-152118800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:152117200-152118800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:152117200-152118800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:152117200-152118800	Active TSS	Aorta	Aorta
30	chr2:152117200-152118800	Active TSS	Brain Hippocampus Middle	brain
31	chr2:152117200-152118800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:152117200-152118800	Active TSS	Fetal Intestine Large	intestine
33	chr2:152117200-152118800	Active TSS	Fetal Muscle Trunk	muscle
34	chr2:152117200-152118800	Active TSS	Ovary	ovary
35	chr2:152117200-152118800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr2:152117200-152118800	Active TSS	Thymus	Thymus
37	chr2:152117200-152119000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:152117400-152118400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:152117400-152118400	Active TSS	HUVEC	blood vessel
40	chr2:152117400-152118600	Active TSS	H9 Cell Line	embryonic stem cell
41	chr2:152117400-152118600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:152117400-152118600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:152117400-152118600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:152117400-152118600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:152117400-152118600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:152117400-152118600	Active TSS	Brain Angular Gyrus	brain
47	chr2:152117400-152118600	Active TSS	Brain Cingulate Gyrus	brain
48	chr2:152117400-152118600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:152117400-152118600	Active TSS	Brain Substantia Nigra	brain
50	chr2:152117400-152118600	Active TSS	Skeletal Muscle Female	skeletal muscle

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