Variant report

Variant	rs4417044
Chromosome Location	chr1:161888955-161888956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161881420..161885079-chr1:161887506..161889889,3	K562	blood:
2	chr1:161879997..161882988-chr1:161887506..161891115,3	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10159039	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10436881	0.81[YRI][hapmap]
rs10733046	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10737517	0.91[ASN][1000 genomes]
rs10737518	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753679	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753685	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753686	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800106	0.89[ASN][1000 genomes]
rs10800109	0.90[ASN][1000 genomes]
rs10800137	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800157	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918214	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918215	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918224	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918225	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918227	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918279	0.89[ASN][1000 genomes]
rs10918290	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024729	0.90[YRI][hapmap]
rs12045333	0.89[YRI][hapmap]
rs12086247	0.81[YRI][hapmap]
rs12096504	0.87[ASN][1000 genomes]
rs12142836	0.91[ASN][1000 genomes]
rs12405111	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs12562272	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1354370	0.90[YRI][hapmap]
rs1503807	0.90[YRI][hapmap]
rs16827987	0.91[ASN][1000 genomes]
rs16860777	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs2070151	0.92[ASW][hapmap]
rs2089083	0.90[YRI][hapmap]
rs2271010	0.90[YRI][hapmap]
rs2340715	0.90[YRI][hapmap]
rs2340823	0.92[ASW][hapmap]
rs2341470	0.89[ASN][1000 genomes]
rs2341480	0.91[ASN][1000 genomes]
rs2341481	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490442	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2499845	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2499846	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2499847	0.84[ASN][1000 genomes]
rs2499848	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2499849	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2499850	0.84[ASN][1000 genomes]
rs2499852	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2499854	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2880056	1.00[ASW][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs4570397	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656340	0.89[ASN][1000 genomes]
rs4657100	1.00[ASW][hapmap]
rs4657101	0.83[ASW][hapmap]
rs4657102	0.83[ASW][hapmap]
rs4657122	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4657124	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4657125	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4657126	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656937	0.91[ASN][1000 genomes]
rs6670429	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6671373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683712	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695574	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7417576	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513303	0.90[YRI][hapmap]
rs7514053	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514226	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7516104	0.91[ASN][1000 genomes]
rs7522210	0.89[ASN][1000 genomes]
rs7530997	0.92[ASW][hapmap]
rs7534981	0.82[YRI][hapmap]
rs7537054	0.83[YRI][hapmap]
rs9283413	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287066	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9482	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9659616	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3440913	chr1:161864485-161897210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3353497	chr1:161864505-161897180	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv946414	chr1:161887945-161889906	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4417044	CD84	cis	parietal	SCAN
rs4417044	PYHIN1	cis	cerebellum	SCAN
rs4417044	ATF6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:161861600-161891400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:161861600-161906400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:161877400-161891400	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:161880000-161890600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:161880000-161891600	Weak transcription	Fetal Stomach	stomach
8	chr1:161880600-161890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:161880600-161892000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:161880800-161891200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:161880800-161891200	Weak transcription	NHLF	lung
12	chr1:161881000-161890600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:161881600-161898800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:161881600-161912000	Weak transcription	Aorta	Aorta
15	chr1:161881800-161890400	Weak transcription	HSMMtube	muscle
16	chr1:161882200-161889400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:161883000-161898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:161883200-161916000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:161883400-161896200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:161883400-161928200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:161884000-161890400	Weak transcription	NHDF-Ad	bronchial
22	chr1:161884200-161890200	Weak transcription	HMEC	breast
23	chr1:161884200-161910800	Weak transcription	HepG2	liver
24	chr1:161884400-161896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:161884600-161927600	Weak transcription	NHEK	skin
26	chr1:161884800-161890400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:161884800-161922600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:161885000-161890800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:161885000-161910600	Weak transcription	Gastric	stomach
30	chr1:161885000-161914400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:161885000-161928000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:161885200-161890400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:161885200-161890400	Weak transcription	NH-A	brain
34	chr1:161885200-161891000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:161885200-161891600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:161885200-161891600	Weak transcription	HUVEC	blood vessel
37	chr1:161885200-161903600	Weak transcription	Thymus	Thymus
38	chr1:161885200-161911800	Weak transcription	Left Ventricle	heart
39	chr1:161885400-161890200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:161885400-161890400	Weak transcription	HSMM	muscle
41	chr1:161885400-161890400	Weak transcription	Osteobl	bone
42	chr1:161885400-161896000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:161885400-161903600	Weak transcription	Fetal Thymus	thymus
44	chr1:161885400-161906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:161885600-161890800	Weak transcription	Fetal Lung	lung
46	chr1:161885600-161893000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:161885600-161896200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:161885600-161899000	Weak transcription	Ovary	ovary
49	chr1:161885600-161905000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:161885800-161890600	Weak transcription	Fetal Muscle Leg	muscle

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