Variant report

Variant	rs1662172
Chromosome Location	chr11:4117155-4117156
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	chr11:3857735..3860667-chr11:4115366..4118226,4	K562	blood:
2	chr11:3861866..3863441-chr11:4116962..4119741,2	MCF-7	breast:
3	chr11:4116202..4117899-chr11:4118829..4121335,2	MCF-7	breast:
4	chr11:4116176..4118411-chr11:4121664..4124693,3	MCF-7	breast:
5	chr11:4116211..4118977-chr11:4131945..4133652,2	K562	blood:
6	chr11:3829231..3830814-chr11:4115429..4117638,2	K562	blood:
7	chr11:3860690..3862593-chr11:4116069..4117581,2	MCF-7	breast:
8	chr11:4116269..4118457-chr11:4145281..4147453,2	MCF-7	breast:
9	chr11:3839155..3841334-chr11:4117148..4119265,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177105	Chromatin interaction
ENSG00000148985	Chromatin interaction
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10835613	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835632	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835650	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11030907	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11030967	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11031096	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604649	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12292367	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364664	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12803023	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs1372805	0.82[CHD][hapmap];0.91[MEX][hapmap]
rs1980412	0.84[MEX][hapmap]
rs2119986	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304891	0.82[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs2412344	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2735691	0.84[MEX][hapmap]
rs2920144	0.87[MEX][hapmap]
rs2959068	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs2959081	0.83[MEX][hapmap]
rs54816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67074167	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7110060	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7124301	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs725518	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs725519	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs747883	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active 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	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1662172	TRIM21	cis	cerebellum	SCAN
rs1662172	OR51E2	cis	cerebellum	SCAN
rs1662172	OR52I2	cis	parietal	SCAN
rs1662172	RRM1	cis	cerebellum	SCAN
rs1662172	RRM1	cis	Artery Tibial	GTEx
rs1662172	KRTAP5-4	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4115000-4117200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:4115000-4117200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr11:4115000-4117400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr11:4115000-4117400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr11:4115000-4117400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:4115000-4117600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:4115200-4117200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:4115200-4117200	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr11:4115200-4117400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:4115200-4117400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:4115200-4117400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:4115200-4117400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:4115200-4117600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr11:4115200-4117600	Active TSS	Right Atrium	heart
15	chr11:4115400-4117200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:4115400-4117200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:4115400-4117200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:4115400-4117200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:4115400-4117200	Active TSS	Psoas Muscle	Psoas
20	chr11:4115400-4118200	Active TSS	GM12878-XiMat	blood
21	chr11:4115600-4117400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr11:4116200-4117200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr11:4116400-4117200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr11:4116400-4117200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr11:4116400-4117200	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr11:4116400-4117600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr11:4116400-4117800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr11:4116600-4117200	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr11:4116600-4117200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr11:4116600-4117200	Flanking Active TSS	Liver	Liver
31	chr11:4116600-4117200	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr11:4116600-4117200	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr11:4116600-4117200	Flanking Active TSS	Fetal Brain Male	brain
34	chr11:4116600-4117200	Flanking Active TSS	Gastric	stomach
35	chr11:4116600-4117200	Flanking Active TSS	Pancreas	Pancrea
36	chr11:4116600-4117200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr11:4116600-4117400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:4116600-4117400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr11:4116600-4117400	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr11:4116600-4117400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr11:4116600-4117400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr11:4116600-4117400	Enhancers	Small Intestine	intestine
43	chr11:4116600-4117600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:4116600-4117600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr11:4116600-4117600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr11:4116600-4117600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:4116600-4117600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr11:4116600-4117600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:4116600-4117600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:4116600-4117600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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