Variant report

Variant	rs4757638
Chromosome Location	chr11:18312953-18312954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18307338..18310336-chr11:18312698..18315910,3	K562	blood:
2	chr11:18311413..18313148-chr11:18342524..18345132,2	K562	blood:

Variant related genes	Relation type
ENSG00000110768	Chromatin interaction
ENSG00000110756	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10766467	0.81[EUR][1000 genomes]
rs10766469	0.82[EUR][1000 genomes]
rs10766471	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832920	0.91[CEU][hapmap]
rs11024605	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024606	0.81[EUR][1000 genomes]
rs11024607	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024608	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024609	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024610	0.80[ASN][1000 genomes]
rs11024611	0.80[ASN][1000 genomes]
rs11024612	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024613	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11024614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024615	0.80[ASN][1000 genomes]
rs11024621	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024622	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12224608	0.83[JPT][hapmap]
rs12294486	0.82[EUR][1000 genomes]
rs1869786	0.80[ASN][1000 genomes]
rs1869787	0.80[ASN][1000 genomes]
rs2037867	0.90[CEU][hapmap]
rs2305564	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2305565	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403254	0.92[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs3781944	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs3802967	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs4150581	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs4150606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150644	0.92[ASN][1000 genomes]
rs4366463	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4586132	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4596	0.92[CEU][hapmap]
rs4756938	0.80[ASN][1000 genomes]
rs4757639	0.80[ASN][1000 genomes]
rs60677587	0.80[ASN][1000 genomes]
rs7113249	0.83[JPT][hapmap]
rs7122032	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7128017	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7128146	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs73430865	0.80[ASN][1000 genomes]
rs73430866	0.80[ASN][1000 genomes]
rs73430881	0.80[ASN][1000 genomes]
rs73430888	0.80[ASN][1000 genomes]
rs73430894	0.80[ASN][1000 genomes]
rs73432712	0.80[ASN][1000 genomes]
rs7478729	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers 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	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4757638	PIK3C2A	cis	cerebellum	SCAN
rs4757638	LDHA	cis	parietal	SCAN
rs4757638	MRGPRX2	cis	cerebellum	SCAN
rs4757638	GTF2H1	cis	cerebellum	SCAN
rs4757638	SAA2	cis	cerebellum	SCAN
rs4757638	GTF2H1	cis	parietal	SCAN
rs4757638	HPS5	cis	parietal	SCAN
rs4757638	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4757638	HPS5	cis	cerebellum	SCAN
rs4757638	LDHAL6A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18287600-18334000	Weak transcription	Right Atrium	heart
2	chr11:18291800-18314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18292000-18314800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:18296800-18315400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:18297400-18328400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:18298200-18333800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:18298600-18326200	Strong transcription	Liver	Liver
8	chr11:18298800-18314200	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr11:18298800-18327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:18298800-18331600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:18299200-18322000	Strong transcription	HMEC	breast
12	chr11:18299200-18332400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:18299600-18326200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:18299600-18334200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:18300000-18320600	Strong transcription	Left Ventricle	heart
16	chr11:18300000-18328600	Weak transcription	Stomach Mucosa	stomach
17	chr11:18300000-18334400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:18300200-18320800	Strong transcription	Fetal Intestine Large	intestine
19	chr11:18300200-18323600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:18300200-18333600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:18300200-18334000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:18300200-18334800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:18300600-18323600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:18300600-18331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:18300600-18332600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:18300600-18333200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:18300600-18334000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:18300800-18328400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:18300800-18330200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:18300800-18333000	Strong transcription	Dnd41	blood
32	chr11:18301000-18320600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:18301000-18321800	Strong transcription	HSMM	muscle
34	chr11:18301000-18328000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:18301000-18334400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:18301200-18324400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:18302000-18315600	Weak transcription	Fetal Heart	heart
38	chr11:18302000-18325000	Strong transcription	HSMMtube	muscle
39	chr11:18302200-18316600	Strong transcription	Brain Hippocampus Middle	brain
40	chr11:18302200-18333000	Strong transcription	Adipose Nuclei	Adipose
41	chr11:18302400-18316800	Strong transcription	Fetal Stomach	stomach
42	chr11:18303000-18321600	Strong transcription	Placenta	Placenta
43	chr11:18303000-18321600	Strong transcription	A549	lung
44	chr11:18303000-18327000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:18303000-18334800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:18303200-18316600	Strong transcription	GM12878-XiMat	blood
47	chr11:18303200-18322600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:18303200-18325600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr11:18303200-18334800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:18303400-18335000	Strong transcription	Primary T cells fromperipheralblood	blood

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