Variant report

Variant	rs6604026
Chromosome Location	chr1:93303603-93303604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:93303001-93304270	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:93303383-93303816	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:93303468-93303864	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:93303378-93303844	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:93301729-93304411	K562	blood:	n/a	n/a
6	POLR2A	chr1:93302966-93303919	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:93301994-93304325	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:93303274-93305956	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:93303221-93303789	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:93301951-93304524	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:93303370-93303855	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:93301157-93303829	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:93303476-93303729	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:93303312-93303703	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:93302592-93304325	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:93301434-93307185	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:93303363-93304272	K562	blood:	n/a	n/a
18	POLR2A	chr1:93303487-93303834	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:93303257-93303724	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:93301402-93304643	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr1:93303348-93304208	A549	lung:	n/a	n/a
22	POLR2A	chr1:93303586-93303735	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr1:93302440-93303763	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:93303180-93303916	K562	blood:	n/a	n/a
25	POLR2A	chr1:93303382-93303823	K562	blood:	n/a	n/a
26	POLR2A	chr1:93303166-93307156	K562	blood:	n/a	n/a
27	NFATC1	chr1:93303382-93304187	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:93303462-93303771	K562	blood:	n/a	n/a
29	POLR2A	chr1:93301952-93304401	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:93301216-93310285	K562	blood:	n/a	n/a
31	HEY1	chr1:93303463-93303812	K562	blood:	n/a	n/a
32	POLR2A	chr1:93301817-93304585	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:93303264-93304423	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr1:93302382-93303875	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
2	chr1:93214862..93218519-chr1:93302722..93305780,4	K562	blood:
3	chr1:93303345..93305385-chr1:93311213..93313203,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA66	TF binding region
ENSG00000207022	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000234202	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10874745	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164820	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11164825	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11582791	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	1.00[ASN][1000 genomes]
rs11586570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11803097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062315	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081675	1.00[JPT][hapmap]
rs12082659	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731107	1.00[JPT][hapmap]
rs12743005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746956	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	1.00[JPT][hapmap]
rs12749786	1.00[CHB][hapmap]
rs12750269	0.91[EUR][1000 genomes]
rs17381426	1.00[CHB][hapmap]
rs1854797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2893226	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.86[ASN][1000 genomes]
rs34098754	0.86[ASN][1000 genomes]
rs34168045	0.85[EUR][1000 genomes]
rs34202284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Multiple sclerosis	19525955	GWAS catalog
Multiple sclerosis	17660530	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6604026	FAM69A	cis	Artery Tibial	GTEx
rs6604026	KIAA1107	cis	cerebellum	SCAN
rs6604026	FAM69A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93299200-93303800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:93299200-93305400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
3	chr1:93299200-93306200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:93299200-93310400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:93299400-93307200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:93299400-93309200	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:93299600-93304400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:93299600-93306000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:93299600-93306600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:93299600-93309000	Weak transcription	Esophagus	oesophagus
11	chr1:93299600-93309800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:93299600-93310000	Strong transcription	Placenta	Placenta
13	chr1:93299600-93310400	Strong transcription	Fetal Thymus	thymus
14	chr1:93299800-93304200	Weak transcription	Gastric	stomach
15	chr1:93299800-93304400	Genic enhancers	NHDF-Ad	bronchial
16	chr1:93299800-93310600	Strong transcription	Fetal Intestine Large	intestine
17	chr1:93299800-93311600	Strong transcription	Fetal Muscle Leg	muscle
18	chr1:93300000-93303800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:93300000-93305000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:93300000-93305800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:93300000-93306000	Genic enhancers	Primary T cells from cord blood	blood
22	chr1:93300000-93306200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:93300000-93309800	Strong transcription	Thymus	Thymus
24	chr1:93300000-93310000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:93300000-93310000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:93300000-93310200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:93300200-93305400	Genic enhancers	HepG2	liver
28	chr1:93300200-93306000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:93300200-93306000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:93300200-93306600	Strong transcription	Fetal Kidney	kidney
31	chr1:93300200-93308000	Strong transcription	Colonic Mucosa	Colon
32	chr1:93300200-93309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:93300200-93310000	Strong transcription	HSMMtube	muscle
34	chr1:93300200-93310200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:93300200-93310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:93300400-93305000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:93300400-93305000	Strong transcription	Fetal Lung	lung
38	chr1:93300400-93305800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:93300400-93306600	Strong transcription	Lung	lung
40	chr1:93300400-93310000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:93300400-93316000	Strong transcription	Primary B cells from cord blood	blood
42	chr1:93300600-93304200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:93300600-93304400	Genic enhancers	Osteobl	bone
44	chr1:93300600-93305200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:93300600-93308800	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr1:93300600-93309200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:93300600-93310000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:93300800-93304400	Genic enhancers	NHEK	skin
49	chr1:93300800-93304800	Weak transcription	Ovary	ovary
50	chr1:93300800-93304800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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