Variant report

Variant	rs2273938
Chromosome Location	chr1:227922640-227922641
allele	A/G
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	MAX	chr1:227922506-227923248	HepG2	liver:	n/a	chr1:227922598-227922607
2	POLR2A	chr1:227922095-227923743	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:227922324-227923419	K562	blood:	n/a	n/a
4	TCF12	chr1:227922345-227923575	A549	lung:	n/a	chr1:227922625-227922635
5	MAX	chr1:227922265-227923415	MCF-7	breast:	n/a	chr1:227922598-227922607
6	POLR2A	chr1:227922205-227924256	PBDE	blood:	n/a	n/a
7	SIN3AK20	chr1:227922266-227923575	K562	blood:	n/a	n/a
8	SIN3AK20	chr1:227922540-227923490	PANC-1	pancreas:	n/a	n/a
9	ELK1	chr1:227922528-227923283	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:227922479-227923559	A549	lung:	n/a	n/a
11	GABPA	chr1:227922604-227923323	SK-N-SH	brain:	n/a	n/a
12	MYC	chr1:227922282-227923383	NB4	blood:	n/a	chr1:227922598-227922607
13	TCF12	chr1:227922612-227923347	ECC-1	luminal epithelium:	n/a	chr1:227922625-227922635
14	MAZ	chr1:227922175-227924196	IMR90	lung:	n/a	chr1:227922598-227922607
15	POLR2A	chr1:227922135-227923848	HepG2	liver:	n/a	n/a
16	MAX	chr1:227922166-227923527	A549	lung:	n/a	chr1:227922598-227922607
17	POLR2A	chr1:227922511-227923454	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:227921936-227924227	MCF10A-Er-Src	breast:	n/a	n/a
19	E2F6	chr1:227922621-227923210	K562	blood:	n/a	chr1:227922700-227922710
20	REST	chr1:227922234-227923744	H1-neurons	neurons:	n/a	chr1:227922319-227922339
21	POLR2A	chr1:227922584-227923464	H1-neurons	neurons:	n/a	n/a
22	ZBTB7A	chr1:227922634-227923321	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr1:227922334-227923568	GM19099	blood:	n/a	n/a
24	POLR2A	chr1:227922323-227923444	GM12892	blood:	n/a	n/a
25	E2F6	chr1:227922564-227923472	A549	lung:	n/a	chr1:227923374-227923386 chr1:227922700-227922710
26	GABPA	chr1:227922599-227923347	MCF-7	breast:	n/a	n/a
27	POLR2A	chr1:227922489-227923664	GM15510	blood:	n/a	n/a
28	HCFC1	chr1:227922209-227923627	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:227922298-227923555	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:227922370-227923611	GM18951	blood:	n/a	n/a
31	MYC	chr1:227922625-227923351	A549	lung:	n/a	n/a
32	YY1	chr1:227922592-227923339	HepG2	liver:	n/a	chr1:227922699-227922708
33	TAF1	chr1:227922391-227923413	HepG2	liver:	n/a	n/a
34	EP300	chr1:227922559-227923371	ECC-1	luminal epithelium:	n/a	chr1:227922697-227922706
35	MTA3	chr1:227922583-227923355	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:227922633-227923597	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:227922180-227923715	GM12892	blood:	n/a	n/a
38	MXI1	chr1:227921582-227923837	IMR90	lung:	n/a	n/a
39	POLR2A	chr1:227922290-227923402	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:227921962-227923649	PFSK-1	brain:	n/a	n/a
41	MYC	chr1:227922283-227923324	K562	blood:	n/a	chr1:227922598-227922607
42	POLR2A	chr1:227922317-227923605	GM18505	blood:	n/a	n/a
43	KAP1	chr1:227922380-227923230	HEK293	kidney:	n/a	n/a
44	POLR2A	chr1:227922244-227923694	GM19193	blood:	n/a	n/a
45	POLR2A	chr1:227922177-227923630	PANC-1	pancreas:	n/a	n/a
46	MAX	chr1:227922341-227923346	ECC-1	luminal epithelium:	n/a	chr1:227922598-227922607
47	TAF1	chr1:227922598-227923511	ECC-1	luminal epithelium:	n/a	n/a
48	GABPA	chr1:227922461-227923468	K562	blood:	n/a	n/a
49	POLR2A	chr1:227922188-227923639	Hela-S3	cervix:	n/a	n/a
50	MXI1	chr1:227922426-227923300	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227921116..227923050-chr1:228289460..228292114,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227750240..227752795-chr1:227921793..227923560,2	K562	blood:
4	chr1:227921956..227924183-chr1:227932541..227935696,3	MCF-7	breast:
5	chr1:227922541..227923238-chr20:21283483..21284425,2	HCT-116	colon:
6	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
7	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

Variant related genes	Relation type
SNAP47	TF binding region
JMJD4	TF binding region
ENSG00000181450	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000088930	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12064596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093611	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236358	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57892813	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61521615	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674275	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688900	0.80[AMR][1000 genomes]
rs6695545	0.82[AMR][1000 genomes]
rs66969031	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67502955	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72632835	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632836	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv3375515	chr1:227921854-227924702	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:227921600-227923000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:227921600-227923600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:227921600-227923600	Active TSS	Placenta Amnion	Placenta Amnion
5	chr1:227921600-227924200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:227921600-227924200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:227921800-227922800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr1:227921800-227922800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr1:227921800-227923800	Active TSS	GM12878-XiMat	blood
10	chr1:227921800-227924200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:227921800-227924200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:227921800-227924200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:227921800-227924200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:227921800-227924200	Active TSS	A549	lung
15	chr1:227922000-227922800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr1:227922000-227922800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:227922000-227922800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:227922000-227923400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:227922000-227923600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:227922000-227923600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:227922000-227923600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:227922000-227923600	Active TSS	Psoas Muscle	Psoas
23	chr1:227922000-227923800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:227922000-227923800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr1:227922000-227923800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:227922000-227923800	Active TSS	Ovary	ovary
27	chr1:227922000-227923800	Active TSS	Hela-S3	cervix
28	chr1:227922000-227923800	Active TSS	K562	blood
29	chr1:227922000-227924000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:227922000-227924000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:227922000-227924000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:227922000-227924000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:227922000-227924000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr1:227922000-227924000	Active TSS	Fetal Kidney	kidney
35	chr1:227922000-227924000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:227922000-227924200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:227922000-227924200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:227922200-227922800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:227922200-227923600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:227922200-227923600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:227922200-227923600	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr1:227922200-227923600	Active TSS	Osteobl	bone
43	chr1:227922200-227923800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:227922200-227923800	Active TSS	Aorta	Aorta
45	chr1:227922200-227923800	Active TSS	HSMMtube	muscle
46	chr1:227922200-227923800	Active TSS	NHEK	skin
47	chr1:227922200-227923800	Active TSS	NHLF	lung
48	chr1:227922200-227924000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:227922200-227924000	Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:227922200-227924000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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