Variant report

Variant	rs10798302
Chromosome Location	chr1:173987798-173987799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:173987762-173987825	MCF10A-Er-Src	breast:	n/a	chr1:173987779-173987787
2	WRNIP1	chr1:173987729-173988014	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173831906..173839548-chr1:173987374..173993282,15	MCF-7	breast:
2	chr1:173836552..173838419-chr1:173986133..173988640,2	K562	blood:
3	chr1:173981372..173983049-chr1:173986515..173988107,2	K562	blood:
4	chr1:173982774..173988202-chr1:173988612..173994506,10	MCF-7	breast:
5	chr1:173971026..173973965-chr1:173986548..173989476,2	K562	blood:
6	chr1:171748445..171750403-chr1:173987079..173989780,2	MCF-7	breast:
7	chr1:173986528..173988374-chr1:174128937..174131109,2	K562	blood:
8	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224977	TF binding region
RC3H1-IT1	TF binding region
ENSG00000208317	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000227373	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10912719	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912722	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12058585	0.87[ASW][hapmap];0.89[MEX][hapmap]
rs12063313	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12066153	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12071784	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs12076799	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12089405	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs12092774	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096785	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097809	0.95[ASN][1000 genomes]
rs12563301	0.87[CHB][hapmap]
rs12563395	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12566651	0.87[ASW][hapmap];0.91[MEX][hapmap]
rs12568409	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1322775	0.87[CHB][hapmap]
rs1322777	0.87[CHB][hapmap]
rs1322780	0.87[CHB][hapmap]
rs13375086	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13376011	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1417186	0.90[YRI][hapmap]
rs16846683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17350956	1.00[YRI][hapmap]
rs17350991	0.89[YRI][hapmap]
rs17353198	0.90[YRI][hapmap]
rs1799876	0.91[CHB][hapmap]
rs1884994	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1951627	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2860841	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs3980286	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs4592301	0.81[EUR][1000 genomes]
rs4650945	0.83[CHB][hapmap]
rs4652169	0.87[CHB][hapmap]
rs4652179	0.90[YRI][hapmap]
rs4652283	0.85[CEU][hapmap]
rs4652298	0.85[CEU][hapmap]
rs4652328	0.85[CEU][hapmap]
rs56247945	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5878	0.87[CHB][hapmap]
rs61547493	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826843	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826844	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61827891	0.83[EUR][1000 genomes]
rs61827894	0.80[EUR][1000 genomes]
rs6425262	0.92[MEX][hapmap]
rs6425267	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6425273	0.83[EUR][1000 genomes]
rs6425275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6661182	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6663875	0.87[CHB][hapmap]
rs6665484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665880	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6668008	0.90[YRI][hapmap]
rs6673632	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6678487	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6686083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6689285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6695887	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs6696076	0.83[CHB][hapmap]
rs6696163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699146	0.87[CHB][hapmap]
rs6703547	0.84[MEX][hapmap]
rs714624	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7413166	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7511780	0.84[ASN][1000 genomes]
rs7514069	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7528380	0.84[MEX][hapmap]
rs7533430	0.83[CHB][hapmap]
rs7538312	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547280	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7547880	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs7553788	0.86[CHB][hapmap]
rs7554915	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs767053	0.87[ASW][hapmap];0.91[MEX][hapmap]
rs9286895	0.87[CHB][hapmap]
rs941989	0.87[CHB][hapmap]
rs9425430	0.87[CHB][hapmap]
rs9425431	0.85[CEU][hapmap]
rs9425433	0.85[CEU][hapmap]
rs9425766	0.87[CHB][hapmap]
rs9661233	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10798302	CENPL	cis	cerebellum	SCAN
rs10798302	C1orf156	cis	parietal	SCAN
rs10798302	SERPINC1	cis	lung	GTEx
rs10798302	SERPINC1	cis	Esophagus Mucosa	GTEx
rs10798302	RABGAP1L	cis	parietal	SCAN
rs10798302	PRDX6	cis	parietal	SCAN
rs10798302	SNORD78	cis	parietal	SCAN
rs10798302	SLC9A11	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:173962200-173989000	Weak transcription	Fetal Kidney	kidney
3	chr1:173962200-173989600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:173962200-173989600	Weak transcription	Aorta	Aorta
5	chr1:173962200-173989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:173962200-173990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:173962400-173987800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:173962600-173988400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:173962600-173988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:173962600-173989400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:173962800-173989800	Weak transcription	Placenta	Placenta
12	chr1:173965000-173989600	Weak transcription	Fetal Thymus	thymus
13	chr1:173966200-173989800	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:173966400-173987800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:173966400-173989600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:173966400-173989800	Weak transcription	Esophagus	oesophagus
17	chr1:173971200-173988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:173976600-173990000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:173977200-173989200	Weak transcription	NH-A	brain
20	chr1:173977800-173988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:173978600-173989200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:173978800-173990200	Weak transcription	Spleen	Spleen
23	chr1:173979000-173987800	Weak transcription	Right Atrium	heart
24	chr1:173979400-173989200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:173979800-173989600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:173981400-173989800	Weak transcription	Pancreas	Pancrea
27	chr1:173983000-173989600	Enhancers	Liver	Liver
28	chr1:173983200-173988400	Weak transcription	NHEK	skin
29	chr1:173983400-173987800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:173983600-173987800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:173984000-173989600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:173984600-173987800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:173984800-173988400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:173984800-173989600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:173985200-173989600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:173985200-173989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:173985400-173987800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:173985800-173989400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:173985800-173989400	Enhancers	HepG2	liver
40	chr1:173986000-173987800	Enhancers	Dnd41	blood
41	chr1:173986000-173988000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:173986000-173988000	Enhancers	Fetal Intestine Small	intestine
43	chr1:173986000-173988600	Enhancers	Brain Cingulate Gyrus	brain
44	chr1:173986000-173988600	Enhancers	Small Intestine	intestine
45	chr1:173986000-173988600	Enhancers	Stomach Mucosa	stomach
46	chr1:173986000-173989000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:173986000-173989000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:173986000-173989000	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:173986000-173989000	Active TSS	GM12878-XiMat	blood
50	chr1:173986000-173989200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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