Variant report

Variant	rs3775220
Chromosome Location	chr4:88014753-88014754
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87843422..87844230-chr4:88014418..88015268,4	MCF-7	breast:
2	chr4:88014659..88016864-chr4:88019432..88023640,4	K562	blood:
3	chr4:87927030..87929816-chr4:88013244..88015675,3	MCF-7	breast:
4	chr4:87854447..87858210-chr4:88013360..88015983,3	K562	blood:
5	chr4:88013784..88016288-chr4:88023619..88027731,5	MCF-7	breast:
6	chr4:87843821..87845327-chr4:88013319..88016028,2	MCF-7	breast:
7	chr4:87926137..87929773-chr4:88012891..88016296,3	K562	blood:
8	chr4:87926587..87929393-chr4:88014126..88017404,4	MCF-7	breast:
9	chr4:87854883..87857377-chr4:88013074..88015993,4	MCF-7	breast:
10	chr4:87843214..87843994-chr4:88014244..88015104,4	MCF-7	breast:
11	chr4:87855131..87857677-chr4:88011511..88016191,4	MCF-7	breast:
12	chr4:87843288..87844189-chr4:88013665..88015393,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10023050	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1037814	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097127	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11946481	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1408	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1674999	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16930	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs17012368	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045592	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];1.00[MEX][hapmap];0.98[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]
rs2125787	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236984	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236985	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236987	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236992	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236993	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236995	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236996	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28432336	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28677145	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2926511	0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs342435	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs342437	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342438	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342452	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342453	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342454	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342456	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342466	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342467	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342468	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342469	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736669	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775214	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775216	0.89[YRI][hapmap]
rs3775217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775223	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442177	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4693156	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];1.00[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]
rs72877984	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7660883	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9998251	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3775220	AFF1	cis	cerebellum	SCAN
rs3775220	SLC10A6	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:88001800-88025200	Weak transcription	Gastric	stomach
8	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
9	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:88005000-88017400	Strong transcription	Dnd41	blood
12	chr4:88007600-88018200	Weak transcription	Thymus	Thymus
13	chr4:88008800-88015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:88009000-88017800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:88009400-88017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:88010200-88015000	Weak transcription	Esophagus	oesophagus
17	chr4:88010200-88018200	Weak transcription	Lung	lung
18	chr4:88010600-88014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:88010600-88015200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:88010600-88018400	Strong transcription	Fetal Thymus	thymus
21	chr4:88011600-88019000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:88011800-88015600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:88011800-88022400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
25	chr4:88012000-88015000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:88012000-88018000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:88012000-88021400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:88012200-88015200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:88012800-88015400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:88012800-88016200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:88013000-88015400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:88013000-88016200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:88013200-88014800	Enhancers	Stomach Mucosa	stomach
34	chr4:88013200-88015200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:88013200-88015200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:88013200-88015400	Enhancers	Osteobl	bone
37	chr4:88013200-88015600	Genic enhancers	Fetal Intestine Small	intestine
38	chr4:88013200-88015600	Strong transcription	Fetal Lung	lung
39	chr4:88013200-88015600	Enhancers	NHEK	skin
40	chr4:88013200-88015800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:88013200-88015800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:88013200-88016400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:88013400-88014800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:88013400-88014800	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:88013400-88015000	Enhancers	HUVEC	blood vessel
46	chr4:88013400-88015200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr4:88013400-88015200	Enhancers	Colon Smooth Muscle	Colon
48	chr4:88013400-88015200	Genic enhancers	GM12878-XiMat	blood
49	chr4:88013400-88015400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:88013400-88015400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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