Variant report

Variant	rs3771888
Chromosome Location	chr2:152138789-152138790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152114819..152117297-chr2:152137988..152139768,2	K562	blood:
2	chr2:152136387..152138845-chr2:152146543..152148937,2	MCF-7	breast:
3	chr2:152124159..152126726-chr2:152137023..152139855,2	K562	blood:
4	chr2:152137402..152140288-chr2:152140945..152142513,2	K562	blood:

Variant related genes	Relation type
ENSG00000123609	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10169816	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176271	0.82[EUR][1000 genomes]
rs10182245	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187344	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1048135	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs11679466	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683487	0.86[CHB][hapmap]
rs11730	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs12617669	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617724	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987765	0.87[CHB][hapmap]
rs13004590	0.86[CHB][hapmap]
rs17798290	0.80[JPT][hapmap]
rs2113509	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs2271811	0.87[CHB][hapmap]
rs2278089	0.82[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs2880489	0.81[EUR][1000 genomes]
rs289828	0.89[EUR][1000 genomes]
rs289829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289833	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289835	0.86[EUR][1000 genomes]
rs34132424	0.82[GIH][hapmap];0.80[TSI][hapmap]
rs35058039	0.81[EUR][1000 genomes]
rs35499578	0.89[EUR][1000 genomes]
rs3771886	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856557	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs387297	0.85[EUR][1000 genomes]
rs4664357	0.81[EUR][1000 genomes]
rs4665150	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs4665159	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665168	0.83[CHB][hapmap]
rs6715393	0.88[EUR][1000 genomes]
rs6718415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744327	0.82[LWK][hapmap];0.92[YRI][hapmap]
rs6747782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3771888	RND3	cis	cerebellum	SCAN
rs3771888	TNFAIP6	cis	parietal	SCAN
rs3771888	TNFAIP6	cis	multi-tissue	Pritchard
rs3771888	RIF1	cis	parietal	SCAN
rs3771888	RBM43	cis	parietal	SCAN
rs3771888	TNFAIP6	cis	Whole Blood	GTEx
rs3771888	RBM43	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152118600-152142800	Weak transcription	Small Intestine	intestine
2	chr2:152118800-152144000	Weak transcription	Stomach Mucosa	stomach
3	chr2:152118800-152144200	Weak transcription	Psoas Muscle	Psoas
4	chr2:152119000-152145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:152119000-152145200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:152119000-152145200	Weak transcription	NHEK	skin
7	chr2:152119000-152145800	Weak transcription	HSMM	muscle
8	chr2:152119400-152142800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:152119400-152144400	Weak transcription	A549	lung
10	chr2:152119400-152144800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:152119400-152145200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:152121200-152145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:152121200-152145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:152124600-152139200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:152125200-152145400	Weak transcription	Aorta	Aorta
16	chr2:152125800-152139200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:152125800-152145200	Weak transcription	Right Ventricle	heart
18	chr2:152126000-152139200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:152126200-152139200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:152126200-152139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:152126200-152139200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:152126200-152139400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:152126200-152139400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:152126200-152139400	Strong transcription	Placenta	Placenta
25	chr2:152126200-152139800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:152126200-152141200	Strong transcription	Dnd41	blood
27	chr2:152126400-152139200	Strong transcription	Primary T cells from cord blood	blood
28	chr2:152126400-152139200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:152126400-152139200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:152126400-152139200	Strong transcription	Adipose Nuclei	Adipose
31	chr2:152126400-152139400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:152126400-152139400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:152126400-152139400	Strong transcription	Liver	Liver
34	chr2:152126400-152139400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:152126400-152139400	Strong transcription	Fetal Thymus	thymus
36	chr2:152126400-152139600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:152126400-152139600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:152126800-152139400	Strong transcription	Primary B cells from cord blood	blood
39	chr2:152126800-152145200	Weak transcription	HMEC	breast
40	chr2:152126800-152145600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:152127000-152145400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:152128000-152144600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:152128400-152145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:152128600-152145200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:152130200-152145600	Weak transcription	Fetal Kidney	kidney
46	chr2:152130600-152144600	Weak transcription	Fetal Lung	lung
47	chr2:152131600-152139200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:152131800-152139200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:152133600-152139200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:152134400-152138800	Weak transcription	Fetal Muscle Leg	muscle

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