Variant report

Variant	rs10511400
Chromosome Location	chr3:120043836-120043837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120042737..120044753-chr3:120045777..120047470,2	MCF-7	breast:
2	chr3:120042251..120044176-chr3:120048760..120051015,2	K562	blood:
3	chr3:120041684..120044051-chr3:120080579..120083270,2	MCF-7	breast:
4	chr3:120042552..120044161-chr3:120066684..120068375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009248	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1085615	0.88[ASN][1000 genomes]
rs12495760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1259339	0.85[CEU][hapmap]
rs1492271	0.85[CEU][hapmap]
rs16831033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2176093	1.00[JPT][hapmap]
rs2272516	1.00[CEU][hapmap]
rs2319674	0.90[ASN][1000 genomes]
rs2943757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34104182	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57086352	0.82[ASN][1000 genomes]
rs58556686	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438577	0.90[ASN][1000 genomes]
rs6770482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771381	0.82[ASN][1000 genomes]
rs6782419	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6791815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6794478	0.85[CEU][hapmap]
rs6803206	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs6803428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803611	0.85[CEU][hapmap]
rs6806659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs701988	0.90[ASN][1000 genomes]
rs72956869	0.82[ASN][1000 genomes]
rs72956871	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7632516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs787191	0.88[ASN][1000 genomes]
rs787195	0.88[ASN][1000 genomes]
rs787198	0.83[CHD][hapmap]
rs787209	0.88[ASN][1000 genomes]
rs787211	0.85[CEU][hapmap]
rs9817398	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9822269	0.85[ASN][1000 genomes]
rs9822672	0.85[ASN][1000 genomes]
rs9874631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Economic and political preferences (feminism/equality)	22566634	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10511400	ILDR1	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
5	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:120033200-120044400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
9	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
11	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:120034600-120052400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:120035200-120049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:120036600-120053600	Weak transcription	Fetal Heart	heart
15	chr3:120037200-120052200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:120038200-120049200	Weak transcription	Fetal Kidney	kidney
17	chr3:120038400-120046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:120038600-120049200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:120038800-120049000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:120038800-120049800	Weak transcription	Fetal Brain Female	brain
21	chr3:120038800-120051600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:120039000-120046600	Weak transcription	Adipose Nuclei	Adipose
23	chr3:120039000-120048000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:120039200-120053600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:120039400-120046600	Weak transcription	Left Ventricle	heart
26	chr3:120039600-120044600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:120039600-120046800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:120039600-120049400	Weak transcription	NHLF	lung
29	chr3:120039800-120049400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:120040000-120046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:120040000-120049000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:120040200-120044400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:120040200-120048400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:120040200-120049000	Weak transcription	HUVEC	blood vessel
35	chr3:120040200-120049200	Weak transcription	Hela-S3	cervix
36	chr3:120040400-120045800	Weak transcription	Primary B cells from cord blood	blood
37	chr3:120040400-120049000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:120040400-120049800	Weak transcription	Brain Angular Gyrus	brain
39	chr3:120040400-120055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:120040400-120056400	Strong transcription	Dnd41	blood
41	chr3:120041000-120046600	Weak transcription	Liver	Liver
42	chr3:120041000-120046600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:120041000-120049000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:120041000-120049200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:120041000-120049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:120041000-120056200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:120041000-120057400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:120041000-120057400	Weak transcription	Small Intestine	intestine
49	chr3:120041000-120058000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:120041200-120045000	Strong transcription	Fetal Thymus	thymus

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