Variant report

Variant	rs55659201
Chromosome Location	chr1:46192545-46192546
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	chr1:46192510..46194017-chr1:46223382..46224964,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1053941	0.85[EUR][1000 genomes]
rs11585275	0.89[EUR][1000 genomes]
rs11587918	0.92[EUR][1000 genomes]
rs11587982	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590549	0.86[EUR][1000 genomes]
rs28412451	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433203	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584711	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014232	0.94[EUR][1000 genomes]
rs41310432	0.85[EUR][1000 genomes]
rs55951835	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56020747	0.86[EUR][1000 genomes]
rs56093189	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56238114	0.87[EUR][1000 genomes]
rs56251392	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58692133	0.85[EUR][1000 genomes]
rs61056720	0.82[EUR][1000 genomes]
rs6429573	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6662572	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662999	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6671239	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72688452	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72688460	0.91[EUR][1000 genomes]
rs7517111	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7541935	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429173	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS 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	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
14	nsv1000498	chr1:46171836-46438252	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	nsv870791	chr1:46182916-46398415	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	38 gene(s)	inside rSNPs	diseases
16	nsv871023	chr1:46184300-46301182	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv998925	chr1:46184925-46353041	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
18	nsv1003986	chr1:46184925-46417621	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
19	nsv1007501	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh 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 lncRNA	39 gene(s)	inside rSNPs	diseases
20	nsv534944	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
21	nsv871763	chr1:46186576-46236098	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
22	nsv1006891	chr1:46189258-46408032	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
23	nsv1009355	chr1:46189258-46463012	Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs55659201	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs55659201	CCDC163P	cis	Muscle Skeletal	GTEx
rs55659201	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs55659201	CCDC163P	cis	lung	GTEx
rs55659201	CCDC163P	cis	Artery Tibial	GTEx
rs55659201	CCDC163P	cis	Nerve Tibial	GTEx
rs55659201	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs55659201	CCDC163P	cis	Esophagus Mucosa	GTEx
rs55659201	CCDC163P	cis	Stomach	GTEx
rs55659201	CCDC163P	cis	Heart Left Ventricle	GTEx
rs55659201	CCDC163P	cis	Whole Blood	GTEx
rs55659201	CCDC163P	cis	Esophagus Muscularis	GTEx
rs55659201	CCDC163P	cis	Thyroid	GTEx
rs55659201	TMEM69	Cis_1M	lymphoblastoid	RTeQTL
rs55659201	CCDC163P	cis	Artery Aorta	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46154600-46206600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:46154800-46192600	Weak transcription	Pancreas	Pancrea
3	chr1:46155000-46215800	Weak transcription	Small Intestine	intestine
4	chr1:46155600-46204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:46155800-46215600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:46156800-46203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:46157400-46209800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:46159800-46194800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:46160800-46215400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:46161000-46196200	Weak transcription	NHEK	skin
11	chr1:46161200-46192800	Weak transcription	Spleen	Spleen
12	chr1:46161200-46196000	Weak transcription	GM12878-XiMat	blood
13	chr1:46161200-46206600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:46162200-46192600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:46163600-46196200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:46163600-46197400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:46163600-46215600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:46165600-46207000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:46174600-46192600	Weak transcription	Thymus	Thymus
20	chr1:46174600-46192800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:46174600-46206400	Weak transcription	Brain Germinal Matrix	brain
22	chr1:46174600-46215600	Weak transcription	Brain Angular Gyrus	brain
23	chr1:46174600-46215600	Weak transcription	Esophagus	oesophagus
24	chr1:46175000-46196400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:46177800-46192800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:46177800-46215600	Weak transcription	Gastric	stomach
27	chr1:46178000-46192600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:46178000-46195800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:46178000-46195800	Weak transcription	Fetal Kidney	kidney
30	chr1:46178000-46209200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:46178000-46209800	Weak transcription	Fetal Brain Male	brain
32	chr1:46178000-46209800	Weak transcription	Lung	lung
33	chr1:46178000-46215600	Weak transcription	Aorta	Aorta
34	chr1:46179600-46206400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:46179600-46209000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:46180400-46192600	Weak transcription	Fetal Thymus	thymus
37	chr1:46180400-46215600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:46180800-46193400	Weak transcription	Dnd41	blood
39	chr1:46181600-46192800	Weak transcription	Placenta	Placenta
40	chr1:46181800-46215600	Weak transcription	Fetal Brain Female	brain
41	chr1:46182000-46192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:46182000-46193200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:46182000-46203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:46182000-46206600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:46182200-46215600	Weak transcription	Left Ventricle	heart
46	chr1:46182400-46206600	Weak transcription	Primary B cells from cord blood	blood
47	chr1:46182400-46206600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:46182600-46195000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:46182800-46192600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:46182800-46195000	Weak transcription	Primary B cells from peripheral blood	blood

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