Variant report

Variant	rs7553229
Chromosome Location	chr1:212662736-212662737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212661275..212664884-chr1:212673911..212677045,3	K562	blood:
2	chr1:212648507..212667078-chr1:212779147..212787651,52	K562	blood:
3	chr1:212645024..212669819-chr1:212778382..212791615,68	K562	blood:
4	chr1:212661862..212663764-chr1:212729767..212731611,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction
ENSG00000260805	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12131037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135668	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12141407	0.89[EUR][1000 genomes]
rs12729438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753186	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12754528	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13374785	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2005230	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292479	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292481	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292482	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3001262	0.96[EUR][1000 genomes]
rs34543166	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36056520	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3951316	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs525176	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557252	0.96[EUR][1000 genomes]
rs591176	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs624387	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626178	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs638527	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653006	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653532	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669813	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6704297	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs679840	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs748517	0.89[EUR][1000 genomes]
rs7513550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517259	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7519767	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7529867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796930	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs806539	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9430096	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
12	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7553229	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212650600-212667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:212655000-212665800	Enhancers	Placenta	Placenta
3	chr1:212655200-212662800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:212657200-212664800	Weak transcription	Spleen	Spleen
5	chr1:212658000-212662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:212658000-212663000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:212658000-212663000	Enhancers	Stomach Mucosa	stomach
8	chr1:212658200-212663000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:212660000-212664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:212660200-212663400	Enhancers	Hela-S3	cervix
11	chr1:212660200-212663600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:212661200-212663000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:212661200-212665800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:212661400-212662800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:212661400-212662800	Enhancers	Colon Smooth Muscle	Colon
16	chr1:212661400-212662800	Enhancers	Lung	lung
17	chr1:212661400-212662800	Flanking Active TSS	A549	lung
18	chr1:212661400-212662800	Enhancers	HSMMtube	muscle
19	chr1:212661400-212663000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:212661400-212663000	Enhancers	Fetal Stomach	stomach
21	chr1:212661400-212663200	Enhancers	Fetal Intestine Large	intestine
22	chr1:212661400-212663200	Enhancers	Fetal Intestine Small	intestine
23	chr1:212661400-212664000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:212661400-212664200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:212661400-212664200	Enhancers	Brain Substantia Nigra	brain
26	chr1:212661400-212664600	Enhancers	Brain Hippocampus Middle	brain
27	chr1:212661400-212664600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:212661600-212662800	Enhancers	Aorta	Aorta
29	chr1:212661600-212662800	Enhancers	HMEC	breast
30	chr1:212661600-212663000	Enhancers	Adipose Nuclei	Adipose
31	chr1:212661600-212663000	Enhancers	Brain Angular Gyrus	brain
32	chr1:212661600-212663000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:212661600-212663000	Enhancers	Fetal Muscle Leg	muscle
34	chr1:212661600-212663000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:212661600-212663000	Enhancers	K562	blood
36	chr1:212661600-212663000	Enhancers	NHEK	skin
37	chr1:212661600-212663400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:212661600-212663800	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:212661600-212664000	Enhancers	Brain Anterior Caudate	brain
40	chr1:212661600-212664200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:212661600-212664400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:212661800-212662800	Enhancers	Fetal Lung	lung
43	chr1:212661800-212663200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:212661800-212663200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:212662000-212662800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:212662000-212662800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:212662000-212663000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:212662000-212663600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:212662000-212663800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:212662000-212664600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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