Variant report

Variant	rs1620734
Chromosome Location	chr1:228297613-228297614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228296659-228297799	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:228296622-228298090	GM12878	blood:	n/a	n/a
3	CTCF	chr1:228297500-228297650	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:228296611-228297758	GM19193	blood:	n/a	n/a
5	EBF1	chr1:228295768-228297810	GM12878	blood:	n/a	chr1:228296439-228296450
6	HMGN3	chr1:228296752-228297717	K562	blood:	n/a	n/a
7	POLR2A	chr1:228296738-228298047	GM12878	blood:	n/a	n/a
8	HCFC1	chr1:228296254-228297617	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:228296779-228298489	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:228297568-228297889	HCT-116	colon:	n/a	n/a
11	CTCF	chr1:228297540-228297690	GM06990	blood:	n/a	n/a
12	POLR2A	chr1:228296604-228297617	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:228297500-228297650	HBMEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:228296584-228297766	PBDE	blood:	n/a	n/a
15	BCL3	chr1:228297558-228298588	GM12878	blood:	n/a	n/a
16	EBF1	chr1:228297464-228297793	GM12878	blood:	n/a	n/a
17	CTCF	chr1:228297560-228297710	AG04449	skin:	n/a	n/a
18	YY1	chr1:228297609-228298115	GM12878	blood:	n/a	n/a
19	MAZ	chr1:228296843-228298267	HepG2	liver:	n/a	chr1:228297140-228297150
20	CTCF	chr1:228297480-228297630	AG04449	skin:	n/a	n/a
21	BHLHE40	chr1:228296814-228297681	GM12878	blood:	n/a	n/a
22	REST	chr1:228296420-228298177	H1-neurons	neurons:	n/a	chr1:228297578-228297591
23	POLR2A	chr1:228296558-228298107	GM12878	blood:	n/a	n/a
24	SP1	chr1:228296723-228297753	H1-hESC	embryonic stem cell:	n/a	chr1:228297140-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297120-228297129 chr1:228297119-228297131 chr1:228297087-228297097 chr1:228297140-228297149 chr1:228297141-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297088-228297097 chr1:228297119-228297131 chr1:228297140-228297150 chr1:228297121-228297130
25	MAX	chr1:228296735-228297708	GM12878	blood:	n/a	chr1:228297140-228297150
26	POLR2A	chr1:228296620-228297746	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr1:228296414-228297721	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:228295964-228297915	K562	blood:	n/a	n/a
29	ZNF263	chr1:228296668-228298204	HEK293-T-REx	kidney:	n/a	chr1:228297526-228297535
30	SIN3A	chr1:228296729-228297657	H1-hESC	embryonic stem cell:	n/a	chr1:228297578-228297591
31	HEY1	chr1:228296449-228297681	K562	blood:	n/a	chr1:228297091-228297106
32	SMARCB1	chr1:228296611-228297796	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:228295080-228298357	HepG2	liver:	n/a	n/a
34	MAZ	chr1:228296785-228298060	K562	blood:	n/a	chr1:228297140-228297150
35	CTCF	chr1:228297500-228297650	HCPEpiC	choroid plexus:	n/a	n/a
36	MXI1	chr1:228296698-228298281	HepG2	liver:	n/a	n/a
37	MXI1	chr1:228296467-228298433	SK-N-SH	brain:	n/a	n/a
38	ZNF143	chr1:228296816-228297795	K562	blood:	n/a	chr1:228297096-228297106 chr1:228297676-228297695
39	POLR2A	chr1:228296490-228298253	IMR90	lung:	n/a	n/a
40	ZBTB7A	chr1:228296631-228297800	ECC-1	luminal epithelium:	n/a	n/a
41	HEY1	chr1:228296635-228297695	HepG2	liver:	n/a	chr1:228297091-228297106
42	CTCF	chr1:228297500-228297650	SK-N-SH_RA	brain:	n/a	n/a
43	ZBTB7A	chr1:228296604-228297890	ECC-1	luminal epithelium:	n/a	n/a
44	TAF1	chr1:228297392-228297713	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr1:228297560-228297710	SK-N-SH_RA	brain:	n/a	n/a
46	EGR1	chr1:228296460-228297687	HCT-116	colon:	n/a	chr1:228297139-228297149 chr1:228297055-228297062 chr1:228297512-228297525 chr1:228297150-228297163 chr1:228297140-228297150 chr1:228297049-228297062
47	CTCF	chr1:228297560-228297710	AG09319	gingival:	n/a	n/a
48	POU2F2	chr1:228296818-228297844	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:228295712-228298089	K562	blood:	n/a	n/a
50	SIN3AK20	chr1:228296623-228297674	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228295623..228298108-chr1:228335544..228338438,2	MCF-7	breast:
2	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
3	chr1:228295479..228298124-chr1:228352385..228354527,2	MCF-7	breast:
4	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
5	chr1:228292983..228294840-chr1:228295520..228297774,2	MCF-7	breast:
6	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:
7	chr1:228193720..228196616-chr1:228296879..228298469,2	MCF-7	breast:
8	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
9	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
10	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
11	chr1:228294689..228298417-chr1:228352364..228354856,6	MCF-7	breast:
12	chr1:228295402..228297803-chr1:228330568..228332279,2	MCF-7	breast:
13	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
14	chr1:228295585..228298584-chr1:228645620..228647778,2	K562	blood:
15	chr1:228297422..228298091-chr17:80023211..80023946,2	HCT-116	colon:
16	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:
17	chr1:228295585..228298429-chr1:228645232..228648455,3	K562	blood:
18	chr1:228295500..228297827-chr1:228593936..228595478,2	K562	blood:
19	chr1:228282584..228285424-chr1:228297065..228299503,2	MCF-7	breast:

Variant related genes	Relation type
MRPL55	TF binding region
C1orf35	TF binding region
ENSG00000154370	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000154342	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000169718	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000198835	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1034792	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1048503	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10916261	0.92[ASN][1000 genomes]
rs10916262	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1094602	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11582265	0.98[EUR][1000 genomes]
rs11582704	0.98[EUR][1000 genomes]
rs11584499	0.86[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11589513	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1188975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188977	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12033088	0.84[EUR][1000 genomes]
rs12048010	0.81[EUR][1000 genomes]
rs13374948	0.82[CHB][hapmap];0.92[ASN][1000 genomes]
rs1745420	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1745422	0.84[EUR][1000 genomes]
rs2070960	1.00[EUR][1000 genomes]
rs2107905	0.81[ASN][1000 genomes]
rs2295995	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3738680	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3738681	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3768329	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3768330	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3820624	0.98[EUR][1000 genomes]
rs41270175	0.84[EUR][1000 genomes]
rs41270177	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4653897	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653906	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs57146523	0.81[EUR][1000 genomes]
rs57657087	0.81[EUR][1000 genomes]
rs61825130	0.81[EUR][1000 genomes]
rs61825131	0.84[EUR][1000 genomes]
rs61825135	0.90[EUR][1000 genomes]
rs6668719	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs708126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72756204	0.81[EUR][1000 genomes]
rs7530253	0.83[AFR][1000 genomes]
rs7537552	0.92[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs7539664	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs822727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860301	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs882451	0.85[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
6	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers 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 miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1620734	MIXL1	cis	cerebellum	SCAN
rs1620734	OBSCN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228295800-228297800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228296000-228298000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:228296000-228298000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:228296000-228298200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:228296200-228297800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:228296200-228297800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:228296200-228297800	Bivalent/Poised TSS	HepG2	liver
8	chr1:228296200-228298000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228296200-228298200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:228296400-228297800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr1:228296400-228297800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:228296400-228297800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:228296400-228297800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:228296400-228297800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:228296400-228297800	Active TSS	Fetal Intestine Large	intestine
16	chr1:228296400-228297800	Active TSS	Gastric	stomach
17	chr1:228296400-228297800	Active TSS	Left Ventricle	heart
18	chr1:228296400-228298000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:228296400-228298000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:228296400-228298000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:228296400-228298000	Active TSS	Aorta	Aorta
22	chr1:228296400-228298000	Active TSS	Ovary	ovary
23	chr1:228296400-228298000	Active TSS	Psoas Muscle	Psoas
24	chr1:228296400-228298000	Active TSS	GM12878-XiMat	blood
25	chr1:228296400-228298000	Active TSS	HMEC	breast
26	chr1:228296400-228298000	Active TSS	NHDF-Ad	bronchial
27	chr1:228296400-228298200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:228296600-228297800	Active TSS	Fetal Intestine Small	intestine
29	chr1:228296600-228298000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:228296600-228298000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:228296600-228298000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:228296600-228298000	Active TSS	Esophagus	oesophagus
33	chr1:228296600-228298000	Active TSS	Fetal Kidney	kidney
34	chr1:228296600-228298000	Active TSS	Lung	lung
35	chr1:228296600-228298000	Active TSS	Small Intestine	intestine
36	chr1:228296600-228298000	Active TSS	NHLF	lung
37	chr1:228296600-228298200	Active TSS	Placenta Amnion	Placenta Amnion
38	chr1:228296600-228298200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:228296600-228298200	Active TSS	HSMMtube	muscle
40	chr1:228296600-228298400	Active TSS	Brain Angular Gyrus	brain
41	chr1:228296600-228298400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:228296600-228298400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:228296600-228298600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:228296800-228297800	Active TSS	Brain Anterior Caudate	brain
45	chr1:228296800-228298000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr1:228296800-228298000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:228296800-228298000	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:228296800-228298000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:228296800-228298200	Active TSS	Brain Substantia Nigra	brain
50	chr1:228297000-228297800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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