Variant report

Variant	rs28364665
Chromosome Location	chr1:170044223-170044224
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	KAP1	chr1:170043352-170044382	HEK293	kidney:	n/a	n/a
2	SMC3	chr1:170043572-170044545	GM12878	blood:	n/a	n/a
3	CTCF	chr1:170043447-170044359	K562	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
4	TBL1XR1	chr1:170043418-170044306	K562	blood:	n/a	n/a
5	TBL1XR1	chr1:170043535-170044541	K562	blood:	n/a	n/a
6	MXI1	chr1:170043002-170044283	IMR90	lung:	n/a	n/a
7	CREB1	chr1:170043451-170044223	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr1:170043038-170044623	GM12878	blood:	n/a	n/a
9	NRF1	chr1:170043456-170044286	GM12878	blood:	n/a	chr1:170043852-170043863 chr1:170043854-170043863 chr1:170043882-170043896 chr1:170043881-170043892
10	MYBL2	chr1:170043522-170044243	HepG2	liver:	n/a	chr1:170044056-170044069
11	CTCF	chr1:170043556-170044278	K562	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
12	POLR2A	chr1:170042533-170044483	GM12891	blood:	n/a	n/a
13	RAD21	chr1:170043687-170044295	A549	lung:	n/a	chr1:170043991-170044010 chr1:170043993-170044005
14	RFX5	chr1:170043500-170044265	Hela-S3	cervix:	n/a	n/a
15	EBF1	chr1:170044217-170044676	GM12878	blood:	n/a	n/a
16	STAT3	chr1:170043603-170044481	GM12878	blood:	n/a	n/a
17	CUX1	chr1:170043835-170044977	GM12878	blood:	n/a	chr1:170044699-170044713 chr1:170044698-170044707
18	CTCF	chr1:170043462-170044396	GM12878	blood:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
19	CTCF	chr1:170043433-170044542	A549	lung:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
20	MAZ	chr1:170042977-170044235	IMR90	lung:	n/a	n/a
21	CREB1	chr1:170043414-170044243	HepG2	liver:	n/a	n/a
22	TCF7L2	chr1:170043897-170044288	MCF-7	breast:	n/a	chr1:170044221-170044230 chr1:170044222-170044232 chr1:170044218-170044234 chr1:170044218-170044234 chr1:170044222-170044231 chr1:170044219-170044233
23	MAX	chr1:170043226-170044380	GM12878	blood:	n/a	n/a
24	EP300	chr1:170043392-170044504	GM12878	blood:	n/a	n/a
25	HCFC1	chr1:170042827-170044890	Hela-S3	cervix:	n/a	n/a
26	IRF1	chr1:170043581-170044275	K562	blood:	n/a	chr1:170043989-170044003
27	CTCF	chr1:170043274-170044455	SK-N-SH	brain:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
28	MAZ	chr1:170043134-170044238	K562	blood:	n/a	n/a
29	RCOR1	chr1:170043227-170044263	GM12878	blood:	n/a	n/a
30	E2F4	chr1:170043606-170044259	MCF10A-Er-Src	breast:	n/a	chr1:170043853-170043862
31	STAT3	chr1:170044059-170044434	MCF10A-Er-Src	breast:	n/a	n/a
32	CHD2	chr1:170043568-170044423	K562	blood:	n/a	n/a
33	ARID3A	chr1:170043720-170044272	HepG2	liver:	n/a	n/a
34	MAX	chr1:170043428-170044256	NB4	blood:	n/a	n/a
35	POLR2A	chr1:170043353-170044231	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:170042539-170044633	GM12878	blood:	n/a	n/a
37	CEBPB	chr1:170043807-170044229	K562	blood:	n/a	n/a
38	EP300	chr1:170043311-170044241	K562	blood:	n/a	n/a
39	CTCF	chr1:170043681-170044252	MCF-7	breast:	n/a	chr1:170043995-170044008 chr1:170043993-170044011
40	SP1	chr1:170043358-170044237	A549	lung:	n/a	n/a
41	MAZ	chr1:170043043-170044248	GM12878	blood:	n/a	n/a
42	CREB1	chr1:170043473-170044231	K562	blood:	n/a	n/a
43	HCFC1	chr1:170043489-170044340	K562	blood:	n/a	n/a
44	JUND	chr1:170043458-170044278	K562	blood:	n/a	n/a
45	RCOR1	chr1:170043306-170044278	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:170044150-170044253	ProgFib	skin:	n/a	n/a
47	ZKSCAN1	chr1:170043489-170044269	Hela-S3	cervix:	n/a	n/a
48	TCF7L2	chr1:170043133-170044453	Hela-S3	cervix:	n/a	chr1:170044221-170044230 chr1:170044222-170044232 chr1:170044218-170044234 chr1:170044218-170044234 chr1:170044222-170044231 chr1:170044219-170044233
49	RELA	chr1:170043153-170044371	GM19099	blood:	n/a	n/a
50	POLR2A	chr1:170043385-170044283	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
2	chr1:170037649..170040302-chr1:170043918..170046865,2	K562	blood:

Variant related genes	Relation type
KIFAP3	TF binding region
ENSG00000075945	Chromatin interaction
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10458398	1.00[AMR][1000 genomes]
rs10800487	1.00[AMR][1000 genomes]
rs12027790	1.00[AMR][1000 genomes]
rs16862931	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2272915	1.00[AMR][1000 genomes]
rs6681074	0.98[ASN][1000 genomes]
rs74122311	0.98[ASN][1000 genomes]
rs7533350	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170042000-170044400	Active TSS	NHLF	lung
2	chr1:170042000-170044600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:170042400-170044600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr1:170042600-170044400	Active TSS	Aorta	Aorta
5	chr1:170042600-170044400	Active TSS	Brain Substantia Nigra	brain
6	chr1:170042600-170044400	Active TSS	Fetal Brain Male	brain
7	chr1:170042600-170044400	Active TSS	Fetal Brain Female	brain
8	chr1:170042600-170044400	Active TSS	Fetal Intestine Large	intestine
9	chr1:170042600-170044400	Active TSS	Ovary	ovary
10	chr1:170042600-170044400	Active TSS	Psoas Muscle	Psoas
11	chr1:170042600-170044400	Active TSS	Stomach Mucosa	stomach
12	chr1:170042600-170044400	Active TSS	A549	lung
13	chr1:170042600-170044600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:170042600-170044600	Active TSS	Right Ventricle	heart
15	chr1:170042800-170044400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:170042800-170044400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:170042800-170044400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:170042800-170044400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:170042800-170044400	Active TSS	Brain Anterior Caudate	brain
20	chr1:170042800-170044400	Active TSS	Brain Cingulate Gyrus	brain
21	chr1:170042800-170044600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:170042800-170044600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:170042800-170044600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:170042800-170044600	Active TSS	Right Atrium	heart
25	chr1:170043000-170044400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:170043000-170044400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:170043000-170044400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:170043000-170044400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:170043000-170044400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:170043000-170044400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:170043000-170044400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr1:170043000-170044400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:170043000-170044400	Active TSS	Fetal Kidney	kidney
34	chr1:170043000-170044400	Active TSS	Fetal Muscle Trunk	muscle
35	chr1:170043000-170044400	Active TSS	Placenta	Placenta
36	chr1:170043000-170044400	Active TSS	Left Ventricle	heart
37	chr1:170043000-170044400	Active TSS	HSMM	muscle
38	chr1:170043000-170044400	Active TSS	HSMMtube	muscle
39	chr1:170043000-170044600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:170043000-170044600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:170043000-170044600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:170043000-170044800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:170043200-170044400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:170043200-170044400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr1:170043200-170044400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:170043200-170044400	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr1:170043200-170044600	Active TSS	Rectal Smooth Muscle	rectum
48	chr1:170043400-170044400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr1:170043400-170044400	Active TSS	Fetal Muscle Leg	muscle
50	chr1:170043400-170044400	Active TSS	Fetal Thymus	thymus

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