Variant report

Variant	rs10753193
Chromosome Location	chr1:179334984-179334985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:472)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:472 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr1:179334966-179335251	K562	blood:	n/a	n/a
2	YY1	chr1:179334715-179335438	K562	blood:	n/a	n/a
3	MAX	chr1:179334645-179335560	NB4	blood:	n/a	n/a
4	POLR2A	chr1:179334536-179335456	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:179334667-179335241	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:179334920-179335070	HMF	breast:	n/a	n/a
7	POLR2A	chr1:179334702-179335693	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:179334655-179335510	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr1:179334624-179335261	K562	blood:	n/a	n/a
10	POLR2A	chr1:179334625-179335326	HepG2	liver:	n/a	n/a
11	CTCF	chr1:179334920-179335070	HRPEpiC	eye:	n/a	n/a
12	ELF1	chr1:179334702-179335377	HepG2	liver:	n/a	chr1:179335021-179335033
13	BCL3	chr1:179334455-179335348	A549	lung:	n/a	n/a
14	YY1	chr1:179334795-179335329	ECC-1	luminal epithelium:	n/a	n/a
15	FOSL2	chr1:179334493-179335117	A549	lung:	n/a	n/a
16	MAFK	chr1:179334877-179335024	HepG2	liver:	n/a	n/a
17	SP1	chr1:179334509-179335371	A549	lung:	n/a	n/a
18	GATA3	chr1:179334730-179335325	T-47D	breast:	n/a	n/a
19	ATF2	chr1:179334685-179335334	GM12878	blood:	n/a	n/a
20	EGR1	chr1:179334652-179335382	MCF-7	breast:	n/a	chr1:179334845-179334854
21	POLR2A	chr1:179334975-179335349	A549	lung:	n/a	n/a
22	POLR2A	chr1:179333806-179335727	GM12891	blood:	n/a	n/a
23	FOSL2	chr1:179334867-179335095	A549	lung:	n/a	n/a
24	TAF1	chr1:179334468-179335374	ECC-1	luminal epithelium:	n/a	n/a
25	BCL3	chr1:179334664-179335199	A549	lung:	n/a	n/a
26	TBP	chr1:179334670-179335363	GM12878	blood:	n/a	n/a
27	EP300	chr1:179334670-179335252	GM12878	blood:	n/a	chr1:179334928-179334942
28	HMGN3	chr1:179334727-179335433	K562	blood:	n/a	n/a
29	RCOR1	chr1:179334802-179335382	Hela-S3	cervix:	n/a	n/a
30	CREB1	chr1:179334632-179335457	A549	lung:	n/a	n/a
31	ELF1	chr1:179334736-179335347	A549	lung:	n/a	chr1:179335021-179335033
32	MYC	chr1:179334942-179335282	MCF10A-Er-Src	breast:	n/a	n/a
33	TBL1XR1	chr1:179334770-179335497	K562	blood:	n/a	n/a
34	E2F6	chr1:179334573-179335440	A549	lung:	n/a	chr1:179334842-179334852 chr1:179334845-179334854
35	MAZ	chr1:179334603-179335405	K562	blood:	n/a	n/a
36	MAX	chr1:179334644-179335583	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:179334807-179335373	U87	brain:	n/a	n/a
38	ZNF143	chr1:179334660-179335449	K562	blood:	n/a	chr1:179335018-179335028
39	STAT5A	chr1:179334843-179335489	GM12878	blood:	n/a	n/a
40	RCOR1	chr1:179334791-179335762	K562	blood:	n/a	n/a
41	ARID3A	chr1:179334879-179335197	K562	blood:	n/a	n/a
42	CTCF	chr1:179334940-179335090	HPF	lung:	n/a	n/a
43	ELK1	chr1:179334793-179335487	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:179334392-179335548	GM12878	blood:	n/a	n/a
45	MYC	chr1:179334811-179335153	K562	blood:	n/a	n/a
46	CHD2	chr1:179334742-179335402	GM12878	blood:	n/a	n/a
47	CTCF	chr1:179334940-179335090	GM12865	blood:	n/a	n/a
48	ELF1	chr1:179334679-179335462	MCF-7	breast:	n/a	chr1:179335021-179335033
49	ETS1	chr1:179334937-179335215	A549	lung:	n/a	n/a
50	RFX5	chr1:179334805-179335036	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
3	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
4	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
5	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
6	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
7	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

No data

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000162779	Chromatin interaction
ENSG00000143322	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1060775	1.00[JPT][hapmap]
rs10798672	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798678	0.82[EUR][1000 genomes]
rs10798682	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs10913776	0.81[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10913804	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs10913807	1.00[JPT][hapmap]
rs12122753	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12131398	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs12131400	1.00[JPT][hapmap]
rs12136100	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12140800	0.82[CHD][hapmap]
rs1328596	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1410590	1.00[JPT][hapmap]
rs1831180	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs1928004	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2152319	0.83[CHD][hapmap]
rs3753525	0.83[CHD][hapmap]
rs3753527	0.83[CHD][hapmap]
rs4255343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4297245	0.85[GIH][hapmap]
rs4360482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4421551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4584358	0.82[EUR][1000 genomes]
rs4606280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4625242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4652386	0.82[EUR][1000 genomes]
rs4652404	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6659294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6662859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6696896	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6697280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697285	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6697373	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698201	1.00[JPT][hapmap]
rs7512551	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7514278	0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7518843	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522064	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7529133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535603	0.90[CEU][hapmap]
rs7540732	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541905	0.93[GIH][hapmap]
rs7542099	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928016	1.00[JPT][hapmap]
rs963062	1.00[JPT][hapmap]
rs964982	0.82[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3523650	chr1:179328529-179335027	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv20900	chr1:179329828-179335094	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10753193	TDRD5	cis	parietal	SCAN
rs10753193	SNORD80	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179334000-179336000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:179334000-179336000	Active TSS	GM12878-XiMat	blood
3	chr1:179334200-179335000	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:179334200-179335200	Active TSS	Placenta	Placenta
5	chr1:179334200-179335400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:179334200-179335400	Active TSS	Duodenum Mucosa	Duodenum
7	chr1:179334200-179335400	Active TSS	Rectal Smooth Muscle	rectum
8	chr1:179334200-179335400	Active TSS	HSMMtube	muscle
9	chr1:179334200-179335600	Active TSS	Colon Smooth Muscle	Colon
10	chr1:179334200-179335600	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr1:179334200-179335600	Active TSS	A549	lung
12	chr1:179334200-179335600	Active TSS	HSMM	muscle
13	chr1:179334200-179335800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:179334200-179335800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:179334200-179335800	Active TSS	Colonic Mucosa	Colon
16	chr1:179334200-179336000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:179334200-179336000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:179334200-179336000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:179334400-179335200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:179334400-179335200	Active TSS	HMEC	breast
21	chr1:179334400-179335200	Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:179334400-179335200	Active TSS	NHLF	lung
23	chr1:179334400-179335400	Active TSS	Aorta	Aorta
24	chr1:179334400-179335400	Active TSS	Liver	Liver
25	chr1:179334400-179335400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:179334400-179335400	Active TSS	NH-A	brain
27	chr1:179334400-179335600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:179334400-179335600	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr1:179334400-179335600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:179334400-179335600	Active TSS	Primary T cells from cord blood	blood
31	chr1:179334400-179335600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:179334400-179335600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:179334400-179335600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:179334400-179335600	Active TSS	Adipose Nuclei	Adipose
35	chr1:179334400-179335600	Active TSS	Brain Hippocampus Middle	brain
36	chr1:179334400-179335600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:179334400-179335600	Active TSS	Fetal Brain Female	brain
38	chr1:179334400-179335600	Active TSS	Fetal Kidney	kidney
39	chr1:179334400-179335600	Active TSS	Fetal Lung	lung
40	chr1:179334400-179335600	Active TSS	Fetal Stomach	stomach
41	chr1:179334400-179335600	Active TSS	Gastric	stomach
42	chr1:179334400-179335600	Active TSS	Ovary	ovary
43	chr1:179334400-179335600	Active TSS	Small Intestine	intestine
44	chr1:179334400-179335600	Active TSS	Stomach Mucosa	stomach
45	chr1:179334400-179335600	Active TSS	Hela-S3	cervix
46	chr1:179334400-179335600	Active TSS	NHEK	skin
47	chr1:179334400-179335600	Active TSS	Osteobl	bone
48	chr1:179334400-179335800	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr1:179334400-179335800	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:179334400-179335800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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