Variant report

Variant	rs4497612
Chromosome Location	chr14:78061009-78061010
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	chr14:78059041..78061902-chr14:78067196..78069981,2	K562	blood:
2	chr14:78060053..78062225-chr14:78085684..78087947,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12431525	0.83[ASN][1000 genomes]
rs12431896	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12433198	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12433954	0.83[ASN][1000 genomes]
rs12434701	0.80[ASN][1000 genomes]
rs12436803	0.83[ASN][1000 genomes]
rs176895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176908	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176912	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751876	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17751917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751923	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17752262	1.00[CHB][hapmap]
rs17752707	1.00[MKK][hapmap]
rs17824984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825229	1.00[CHB][hapmap]
rs17825235	1.00[CHB][hapmap]
rs2142187	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2178877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299918	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2364578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886122	1.00[CHB][hapmap]
rs2886132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389286	0.83[ASN][1000 genomes]
rs55697089	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55776552	1.00[AFR][1000 genomes]
rs55799811	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56264628	1.00[AFR][1000 genomes]
rs56286233	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7159486	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4497612	ADCK1	cis	multi-tissue	Pritchard
rs4497612	ADCK1	cis	Whole Blood	GTEx
rs4497612	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
5	chr14:78042600-78061800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:78043800-78061200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr14:78043800-78061800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:78044000-78061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
10	chr14:78048000-78061400	Weak transcription	Fetal Intestine Small	intestine
11	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
12	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr14:78051400-78061400	Weak transcription	Esophagus	oesophagus
14	chr14:78051400-78061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:78051400-78061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
17	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr14:78051600-78063000	Weak transcription	Left Ventricle	heart
19	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
20	chr14:78052000-78061800	Weak transcription	Brain Anterior Caudate	brain
21	chr14:78052200-78062200	Weak transcription	Brain Angular Gyrus	brain
22	chr14:78052600-78061800	Weak transcription	Ovary	ovary
23	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
24	chr14:78055400-78061200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
26	chr14:78056800-78070000	Weak transcription	Gastric	stomach
27	chr14:78057000-78064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:78057000-78065000	Weak transcription	Lung	lung
29	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
30	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr14:78057800-78061400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr14:78057800-78061600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr14:78057800-78065000	Weak transcription	Small Intestine	intestine
34	chr14:78058000-78063600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:78058800-78063800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr14:78059000-78061200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:78059000-78061400	Genic enhancers	HSMM	muscle
38	chr14:78059000-78063800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:78059000-78065800	Weak transcription	Colonic Mucosa	Colon
40	chr14:78059600-78061200	Enhancers	Stomach Mucosa	stomach
41	chr14:78060000-78061400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr14:78060000-78061400	Weak transcription	NHLF	lung
43	chr14:78060000-78062800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:78060200-78061400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr14:78060200-78061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr14:78060400-78061200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr14:78060400-78061200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr14:78060400-78061200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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