Variant report

Variant	rs12063273
Chromosome Location	chr1:173967087-173967088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:173966912-173967098	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr1:173966768-173967487	SK-N-SH	brain:	n/a	n/a
3	KAP1	chr1:173966364-173967096	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173966661..173969075-chr1:173990133..173991820,3	MCF-7	breast:
2	chr1:173835569..173838721-chr1:173965548..173969329,3	K562	blood:
3	chr1:173964310..173967666-chr1:173990049..173993050,6	MCF-7	breast:
4	chr1:173791607..173793893-chr1:173965038..173968720,3	K562	blood:
5	chr1:173966978..173969283-chr1:173971302..173973529,3	K562	blood:

No data

Variant related genes	Relation type
RC3H1	TF binding region
ENSG00000117593	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10158197	1.00[EUR][1000 genomes]
rs10489892	1.00[EUR][1000 genomes]
rs10489893	1.00[EUR][1000 genomes]
rs10912681	1.00[EUR][1000 genomes]
rs10912687	1.00[EUR][1000 genomes]
rs10912688	1.00[EUR][1000 genomes]
rs10912693	1.00[EUR][1000 genomes]
rs10912699	1.00[EUR][1000 genomes]
rs10912700	1.00[EUR][1000 genomes]
rs10912701	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10912707	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912708	1.00[EUR][1000 genomes]
rs10912711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912712	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10912725	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10912742	1.00[EUR][1000 genomes]
rs10912743	1.00[EUR][1000 genomes]
rs10912744	1.00[EUR][1000 genomes]
rs10912748	1.00[EUR][1000 genomes]
rs1135333	1.00[EUR][1000 genomes]
rs12057220	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057440	1.00[EUR][1000 genomes]
rs12058498	1.00[EUR][1000 genomes]
rs12059636	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060967	1.00[EUR][1000 genomes]
rs12061013	1.00[EUR][1000 genomes]
rs12062801	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12063296	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12064818	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065194	1.00[EUR][1000 genomes]
rs12067109	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12068440	1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12070328	1.00[EUR][1000 genomes]
rs12072553	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12077462	1.00[EUR][1000 genomes]
rs12078222	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078262	0.89[AMR][1000 genomes]
rs12078471	1.00[EUR][1000 genomes]
rs12078645	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12078817	1.00[EUR][1000 genomes]
rs12079240	1.00[EUR][1000 genomes]
rs12079274	1.00[EUR][1000 genomes]
rs12079650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12081595	1.00[EUR][1000 genomes]
rs12084213	1.00[EUR][1000 genomes]
rs12084911	1.00[EUR][1000 genomes]
rs12086246	0.92[AFR][1000 genomes]
rs12090507	1.00[EUR][1000 genomes]
rs12092291	1.00[EUR][1000 genomes]
rs12096013	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1322773	1.00[EUR][1000 genomes]
rs1322781	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1570385	1.00[EUR][1000 genomes]
rs16846395	1.00[EUR][1000 genomes]
rs16846398	1.00[EUR][1000 genomes]
rs1956522	1.00[EUR][1000 genomes]
rs2227611	1.00[EUR][1000 genomes]
rs2227622	1.00[EUR][1000 genomes]
rs57586767	1.00[EUR][1000 genomes]
rs59090917	1.00[EUR][1000 genomes]
rs6425256	1.00[EUR][1000 genomes]
rs6673147	1.00[EUR][1000 genomes]
rs6684147	1.00[EUR][1000 genomes]
rs74126415	1.00[EUR][1000 genomes]
rs7550107	1.00[EUR][1000 genomes]
rs874342	1.00[EUR][1000 genomes]
rs9425413	1.00[EUR][1000 genomes]
rs9425414	1.00[EUR][1000 genomes]
rs9425427	1.00[EUR][1000 genomes]
rs9425735	1.00[EUR][1000 genomes]
rs9425768	1.00[EUR][1000 genomes]
rs997165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
4	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv3692957	chr1:173960747-173967521	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
4	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
6	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
7	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
10	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:173952800-173967600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:173953200-173974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:173958400-173967200	Weak transcription	NHLF	lung
14	chr1:173958600-173987200	Weak transcription	Gastric	stomach
15	chr1:173960800-173970400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:173962000-173967400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:173962000-173967600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:173962000-173975000	Weak transcription	Right Ventricle	heart
19	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:173962200-173967200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:173962200-173967200	Weak transcription	Brain Substantia Nigra	brain
22	chr1:173962200-173967200	Weak transcription	Fetal Lung	lung
23	chr1:173962200-173967400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:173962200-173967400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:173962200-173967400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:173962200-173968000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:173962200-173968600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:173962200-173969600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:173962200-173969600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:173962200-173970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:173962200-173970400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:173962200-173970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:173962200-173970400	Weak transcription	Ovary	ovary
34	chr1:173962200-173970600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:173962200-173972200	Weak transcription	Spleen	Spleen
36	chr1:173962200-173974000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:173962200-173974000	Weak transcription	HSMMtube	muscle
38	chr1:173962200-173974200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:173962200-173974200	Weak transcription	HMEC	breast
40	chr1:173962200-173976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:173962200-173976800	Weak transcription	NH-A	brain
42	chr1:173962200-173977200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:173962200-173978400	Weak transcription	Colonic Mucosa	Colon
44	chr1:173962200-173978600	Weak transcription	Lung	lung
45	chr1:173962200-173983200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:173962200-173984200	Weak transcription	Primary T cells from cord blood	blood
47	chr1:173962200-173989000	Weak transcription	Fetal Kidney	kidney
48	chr1:173962200-173989600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:173962200-173989600	Weak transcription	Aorta	Aorta
50	chr1:173962200-173989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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