Variant report

Variant	rs544446
Chromosome Location	chr11:57470844-57470845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57469323..57472017-chr11:57472443..57474700,2	K562	blood:
2	chr11:57467968..57471169-chr11:57473477..57476394,3	MCF-7	breast:
3	chr11:57464857..57467583-chr11:57469531..57471627,4	K562	blood:
4	chr11:57469769..57472099-chr11:57500346..57502166,2	K562	blood:
5	chr11:57432810..57435746-chr11:57470332..57472894,2	MCF-7	breast:
6	chr11:57464857..57467583-chr11:57469531..57471287,2	K562	blood:
7	chr11:57469550..57472113-chr11:57477517..57480022,2	K562	blood:

Variant related genes	Relation type
ENSG00000156603	Chromatin interaction
ENSG00000156599	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10896634	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229087	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs11229115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267146	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12793139	0.89[JPT][hapmap]
rs1424752	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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848445	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs479573	0.86[ASN][1000 genomes]
rs480933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483030	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs486995	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491719	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492131	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501054	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501738	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503037	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504311	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504921	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507946	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509564	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511708	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515939	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs517638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523985	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527140	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[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];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530094	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536673	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537627	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540234	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541245	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549022	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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558653	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567017	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577741	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581217	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58132137	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs594233	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604094	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604344	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];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608648	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609596	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs612688	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61888873	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888880	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624759	0.84[ASN][1000 genomes]
rs627816	0.80[ASN][1000 genomes]
rs628100	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636807	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638864	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640767	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645097	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs647264	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656227	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658183	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666021	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669433	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669950	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675154	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs676205	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7108113	0.84[ASN][1000 genomes]
rs72928102	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs96894	0.81[AFR][1000 genomes];0.80[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv975360	chr11:57466716-57480320	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs544446	OR4C11	cis	cerebellum	SCAN
rs544446	SPRYD5	cis	cerebellum	SCAN
rs544446	YPEL4	cis	lymphoblastoid	seeQTL
rs544446	MED19	cis	Artery Tibial	GTEx
rs544446	MED19	cis	cerebellum	SCAN
rs544446	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57436600-57479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57438600-57478200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:57438800-57473800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr11:57439000-57473400	Strong transcription	Fetal Thymus	thymus
5	chr11:57439000-57477400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:57439400-57473000	Strong transcription	Placenta	Placenta
7	chr11:57439800-57473400	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:57442800-57472800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:57443200-57472600	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:57446600-57474200	Strong transcription	Fetal Intestine Large	intestine
11	chr11:57447000-57473800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:57447800-57474200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:57448000-57472800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:57448000-57473200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:57448200-57474400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:57448400-57472600	Strong transcription	Liver	Liver
17	chr11:57448400-57472600	Strong transcription	Lung	lung
18	chr11:57448400-57472600	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:57448400-57472800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:57448400-57472800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:57448400-57473800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:57448600-57476400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:57449000-57476000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:57449400-57474200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:57449800-57474200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:57450400-57473800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:57451200-57474200	Strong transcription	Fetal Stomach	stomach
28	chr11:57451400-57472600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:57451400-57472800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:57453000-57475200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:57455600-57472800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:57455600-57472800	Strong transcription	Left Ventricle	heart
33	chr11:57458000-57472600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:57458000-57474600	Strong transcription	Fetal Intestine Small	intestine
35	chr11:57458000-57475800	Strong transcription	Thymus	Thymus
36	chr11:57458200-57472800	Strong transcription	Brain Germinal Matrix	brain
37	chr11:57459200-57472600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr11:57459200-57472800	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr11:57459200-57472800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:57459200-57472800	Strong transcription	Colonic Mucosa	Colon
41	chr11:57459200-57473800	Strong transcription	Primary T cells from cord blood	blood
42	chr11:57459200-57476200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:57459400-57473200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:57459600-57471800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:57459800-57472800	Strong transcription	Fetal Lung	lung
46	chr11:57461000-57473400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:57461400-57478400	Weak transcription	Fetal Heart	heart
48	chr11:57462400-57471400	Weak transcription	Fetal Brain Male	brain
49	chr11:57464400-57478800	Weak transcription	Psoas Muscle	Psoas
50	chr11:57465400-57471200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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