Variant report

Variant	rs555412
Chromosome Location	chr3:195804918-195804919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195796379..195810322-chr3:195910077..195926320,43	MCF-7	breast:
2	chr3:195777307..195778970-chr3:195803293..195805251,2	K562	blood:
3	chr3:195793504..195812987-chr3:195901613..195938073,113	K562	blood:
4	chr3:195735405..195738324-chr3:195803817..195806018,2	K562	blood:
5	chr3:195804323..195810515-chr3:195865435..195874009,30	K562	blood:
6	chr3:195801443..195805160-chr3:195868398..195871334,3	MCF-7	breast:
7	chr3:195793504..195812415-chr3:195915832..195927942,46	K562	blood:

No data

Variant related genes	Relation type
ENSG00000222335	Chromatin interaction
ENSG00000163958	Chromatin interaction
ENSG00000224652	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11705886	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915082	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926771	0.82[JPT][hapmap]
rs12631246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632706	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061255	0.82[JPT][hapmap]
rs2010078	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817672	0.80[ASW][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs3862281	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41297495	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300379	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301371	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422772	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528937	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55970879	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56038600	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56224853	0.97[ASN][1000 genomes]
rs57783901	0.82[EUR][1000 genomes]
rs58079878	0.97[ASN][1000 genomes]
rs58365266	0.88[ASN][1000 genomes]
rs714602	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73208092	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73210005	0.97[ASN][1000 genomes]
rs73210008	0.97[ASN][1000 genomes]
rs9829686	0.86[CHB][hapmap]
rs9852883	0.82[AFR][1000 genomes]
rs9867473	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	nsv1010395	chr3:195641908-195848264	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv1820982	chr3:195651349-195835519	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv878170	chr3:195677895-195871388	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
12	nsv1002584	chr3:195734933-195910772	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
14	nsv878172	chr3:195751853-195831098	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
16	nsv1002065	chr3:195769609-195877692	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
18	nsv524410	chr3:195776240-195816195	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
19	nsv461130	chr3:195776240-195907653	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
20	nsv593069	chr3:195776240-195907653	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
21	nsv1005558	chr3:195789462-195919077	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
22	nsv536890	chr3:195789462-195919077	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs555412	IQCG	cis	cerebellum	SCAN
rs555412	IQCG	cis	parietal	SCAN
rs555412	TMEM44	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195773200-195805200	Strong transcription	Fetal Thymus	thymus
2	chr3:195774600-195805400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:195775000-195806600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:195783000-195805800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:195785200-195807400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:195792800-195807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:195794200-195807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:195797600-195806200	Weak transcription	Right Atrium	heart
9	chr3:195798000-195805800	Weak transcription	Fetal Heart	heart
10	chr3:195798200-195807400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:195799000-195807000	Weak transcription	Fetal Brain Male	brain
12	chr3:195799400-195807000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:195800800-195807400	Weak transcription	Fetal Kidney	kidney
14	chr3:195800800-195807600	Weak transcription	Aorta	Aorta
15	chr3:195801000-195805800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:195801000-195805800	Weak transcription	Psoas Muscle	Psoas
17	chr3:195801000-195806600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:195801000-195807400	Weak transcription	HSMM	muscle
19	chr3:195801200-195807400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:195801600-195807400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:195802000-195807400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:195802400-195806600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:195802400-195806600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:195802400-195806800	Weak transcription	A549	lung
25	chr3:195802400-195807200	Weak transcription	NHLF	lung
26	chr3:195802400-195807400	Weak transcription	Fetal Lung	lung
27	chr3:195802400-195807400	Weak transcription	NH-A	brain
28	chr3:195802400-195807400	Weak transcription	NHDF-Ad	bronchial
29	chr3:195802400-195807600	Weak transcription	HSMMtube	muscle
30	chr3:195802600-195805600	Weak transcription	Primary T cells from cord blood	blood
31	chr3:195802600-195805800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:195802600-195805800	Weak transcription	Pancreas	Pancrea
33	chr3:195802600-195805800	Weak transcription	Spleen	Spleen
34	chr3:195802600-195806000	Weak transcription	Brain Germinal Matrix	brain
35	chr3:195802600-195806200	Weak transcription	Gastric	stomach
36	chr3:195802600-195806200	Weak transcription	Small Intestine	intestine
37	chr3:195802600-195806600	Weak transcription	Adipose Nuclei	Adipose
38	chr3:195802600-195806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:195802600-195806600	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:195802600-195806800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:195802800-195805200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:195802800-195806000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:195802800-195806200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:195802800-195806600	Weak transcription	Fetal Brain Female	brain
45	chr3:195802800-195806600	Weak transcription	Fetal Intestine Large	intestine
46	chr3:195802800-195806600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:195802800-195806800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:195802800-195807000	Weak transcription	Colonic Mucosa	Colon
49	chr3:195802800-195807200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:195802800-195807200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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