Variant report

Variant	rs2306862
Chromosome Location	chr11:68177510-68177511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1784235	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2472415	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2508834	0.87[ASN][1000 genomes]
rs314750	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs3736228	1.00[ASW][hapmap];0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3781586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41478448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475712	0.86[ASN][1000 genomes]
rs491347	0.94[JPT][hapmap]
rs546803	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs56400711	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576118	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs583545	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs630225	0.82[CHD][hapmap]
rs640569	0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6591339	0.86[ASN][1000 genomes]
rs667126	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs685095	0.81[ASN][1000 genomes]
rs689179	0.88[ASN][1000 genomes]
rs7102451	0.87[ASN][1000 genomes]
rs7106320	0.88[AMR][1000 genomes]
rs880610	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking 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	17 gene(s)	inside rSNPs	diseases
8	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv897861	chr11:68129606-68196830	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv468618	chr11:68171013-68231240	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3336346	chr11:68175876-68177824	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2306862	MRGPRD	cis	cerebellum	SCAN
rs2306862	VEGFB	cis	cerebellum	SCAN
rs2306862	NDUFS8	cis	parietal	SCAN
rs2306862	CARNS1	cis	cerebellum	SCAN
rs2306862	GAL	cis	parietal	SCAN
rs2306862	CPT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68142600-68179000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:68147400-68181600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:68148600-68196800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:68149600-68180400	Weak transcription	NHLF	lung
5	chr11:68157200-68196600	Weak transcription	NH-A	brain
6	chr11:68157600-68180400	Weak transcription	Osteobl	bone
7	chr11:68165800-68178400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:68167200-68179600	Weak transcription	K562	blood
9	chr11:68167400-68177600	Weak transcription	Brain Anterior Caudate	brain
10	chr11:68167800-68178600	Weak transcription	Psoas Muscle	Psoas
11	chr11:68167800-68181000	Weak transcription	Small Intestine	intestine
12	chr11:68167800-68196600	Weak transcription	Fetal Brain Male	brain
13	chr11:68168400-68185000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:68168400-68189000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:68168600-68181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:68168600-68188800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:68168600-68188800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:68168600-68193600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:68168600-68195600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:68169000-68193600	Strong transcription	Fetal Intestine Small	intestine
21	chr11:68169200-68180200	Strong transcription	Fetal Stomach	stomach
22	chr11:68169200-68180800	Strong transcription	Adipose Nuclei	Adipose
23	chr11:68169400-68181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:68169400-68181600	Strong transcription	Thymus	Thymus
25	chr11:68169400-68196600	Weak transcription	Right Atrium	heart
26	chr11:68169600-68188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:68169600-68196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:68171400-68178000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:68171800-68179600	Weak transcription	Fetal Kidney	kidney
30	chr11:68172200-68178600	Weak transcription	HSMM	muscle
31	chr11:68172200-68180200	Weak transcription	NHDF-Ad	bronchial
32	chr11:68173000-68184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:68173000-68188400	Strong transcription	Dnd41	blood
34	chr11:68173400-68184200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:68173400-68187400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:68173600-68180200	Weak transcription	Fetal Heart	heart
37	chr11:68173800-68177600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:68173800-68177800	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:68173800-68189000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:68174000-68178800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:68174000-68180200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:68174000-68181400	Strong transcription	Fetal Thymus	thymus
43	chr11:68174400-68178200	Weak transcription	Stomach Mucosa	stomach
44	chr11:68174400-68178600	Strong transcription	Liver	Liver
45	chr11:68174400-68179400	Weak transcription	GM12878-XiMat	blood
46	chr11:68174400-68180200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:68174400-68192800	Strong transcription	Fetal Intestine Large	intestine
48	chr11:68174400-68195800	Weak transcription	Primary B cells from cord blood	blood
49	chr11:68174600-68177600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:68174600-68180400	Weak transcription	Muscle Satellite Cultured Cells	--

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