Variant report

Variant	rs4658260
Chromosome Location	chr1:92184673-92184674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92171317..92173686-chr1:92182060..92185039,2	K562	blood:
2	chr1:92184011..92187610-chr1:92188347..92192369,4	K562	blood:
3	chr1:92182554..92184890-chr1:92189322..92192184,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1012069	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[AMR][1000 genomes]
rs11165347	0.88[CEU][hapmap]
rs1542703	0.83[CEU][hapmap];0.90[GIH][hapmap];0.82[AMR][1000 genomes]
rs1542704	0.82[AMR][1000 genomes]
rs17131539	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17884552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007686	0.82[EUR][1000 genomes]
rs2029354	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2029355	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296620	0.87[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296622	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs284877	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs3754014	0.88[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3767569	0.80[GIH][hapmap];1.00[MEX][hapmap]
rs4658261	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699304	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72714444	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4658260	LRRC8C	cis	parietal	SCAN
rs4658260	FAM69A	cis	parietal	SCAN
rs4658260	ARHGAP29	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:92164000-92195000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:92165800-92184800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:92165800-92196800	Weak transcription	Small Intestine	intestine
6	chr1:92166600-92191000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:92167400-92184800	Weak transcription	A549	lung
8	chr1:92168000-92191000	Weak transcription	HUVEC	blood vessel
9	chr1:92169800-92187200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:92171000-92196800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:92171200-92196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:92172800-92197000	Weak transcription	Colonic Mucosa	Colon
13	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:92173600-92185000	Weak transcription	Gastric	stomach
15	chr1:92173600-92197800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:92174400-92191200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:92174600-92184800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:92178000-92185000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:92178800-92184800	Weak transcription	Right Ventricle	heart
20	chr1:92179000-92184800	Weak transcription	Psoas Muscle	Psoas
21	chr1:92179000-92191600	Strong transcription	Placenta	Placenta
22	chr1:92179200-92184800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:92179200-92187800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:92179200-92189800	Weak transcription	Right Atrium	heart
25	chr1:92179400-92184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:92179400-92185000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:92179400-92186800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:92179400-92189800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:92179400-92190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:92179400-92191000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:92179400-92192600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:92179400-92195200	Weak transcription	GM12878-XiMat	blood
33	chr1:92179600-92189800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:92180000-92189600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:92180200-92185000	Strong transcription	Adipose Nuclei	Adipose
36	chr1:92180200-92187200	Strong transcription	Liver	Liver
37	chr1:92180200-92187400	Strong transcription	NHLF	lung
38	chr1:92180200-92188400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:92180400-92187200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:92180800-92187200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:92180800-92187200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:92180800-92189200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:92180800-92194400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:92181600-92187200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:92181600-92189600	Weak transcription	Fetal Heart	heart
46	chr1:92181800-92190600	Strong transcription	NHDF-Ad	bronchial
47	chr1:92182000-92184800	Weak transcription	Spleen	Spleen
48	chr1:92182000-92194400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:92182400-92184800	Weak transcription	Pancreas	Pancrea
50	chr1:92182400-92188000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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