Variant report

Variant	rs6429554
Chromosome Location	chr1:45481551-45481552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45481059-45481873	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:45477475-45482921	K562	blood:	n/a	n/a
3	POLR2A	chr1:45481543-45481571	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:45481273-45482032	K562	blood:	n/a	n/a
5	POLR2A	chr1:45481373-45481650	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:45481358-45482648	K562	blood:	n/a	n/a
7	POLR2A	chr1:45481380-45482603	K562	blood:	n/a	n/a
8	POLR2A	chr1:45481302-45482269	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:45480010-45482910	K562	blood:	n/a	n/a
10	POLR2A	chr1:45480933-45483212	K562	blood:	n/a	n/a
11	POLR2A	chr1:45481426-45482174	K562	blood:	n/a	n/a
12	POLR2A	chr1:45481452-45482603	K562	blood:	n/a	n/a
13	POLR2A	chr1:45481391-45482269	HUVEC	blood vessel:	n/a	n/a
14	CEBPD	chr1:45481226-45482120	K562	blood:	n/a	n/a
15	POLR2A	chr1:45481242-45482170	HepG2	liver:	n/a	n/a
16	PML	chr1:45479742-45482654	K562	blood:	n/a	n/a
17	POLR2A	chr1:45477763-45483536	K562	blood:	n/a	n/a
18	POLR2A	chr1:45481395-45483210	PBDE	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
3	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
4	chr1:45475929..45480621-chr1:45481195..45486078,6	MCF-7	breast:
5	chr1:45185920..45189252-chr1:45480937..45484378,4	K562	blood:
6	chr1:45272933..45277403-chr1:45480865..45483192,4	K562	blood:
7	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
8	chr1:45480602..45482201-chr1:45803688..45807288,4	K562	blood:
9	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
10	chr1:45480075..45485962-chr1:45670647..45674355,5	MCF-7	breast:
11	chr1:45252618..45255680-chr1:45481014..45484053,3	K562	blood:
12	chr1:45265885..45267445-chr1:45480826..45483713,2	K562	blood:
13	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
14	chr1:45476853..45482658-chr1:45802506..45807966,11	K562	blood:
15	chr1:45264684..45267553-chr1:45478723..45482931,4	MCF-7	breast:
16	chr1:45184531..45190715-chr1:45481425..45486664,6	K562	blood:
17	chr1:45478895..45481686-chr1:45791437..45793067,2	MCF-7	breast:
18	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:

No data

Variant related genes	Relation type
HECTD3	TF binding region
ENSG00000186603	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000188396	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2234479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355951	0.87[ASN][1000 genomes]
rs263993	0.87[ASN][1000 genomes]
rs264000	0.87[ASN][1000 genomes]
rs264016	0.87[ASN][1000 genomes]
rs41269097	0.87[ASN][1000 genomes]
rs41269101	0.87[ASN][1000 genomes]
rs41306605	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449870	0.87[ASN][1000 genomes]
rs4660292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474207	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs506691	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs638062	0.87[ASN][1000 genomes]
rs7512137	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533668	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45478400-45483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45478600-45482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45478600-45500000	Weak transcription	Aorta	Aorta
4	chr1:45478800-45482200	Weak transcription	Psoas Muscle	Psoas
5	chr1:45478800-45482600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:45478800-45484000	Weak transcription	Right Atrium	heart
7	chr1:45479000-45482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:45479000-45483400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:45479000-45484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45479000-45484200	Weak transcription	Esophagus	oesophagus
11	chr1:45479000-45485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:45479000-45493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:45479200-45482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:45479200-45484200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:45479400-45481600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:45479400-45481600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:45479400-45481600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:45479400-45481600	Strong transcription	NHEK	skin
19	chr1:45479400-45482000	Strong transcription	Fetal Lung	lung
20	chr1:45479400-45484200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:45479600-45481600	Strong transcription	Placenta	Placenta
22	chr1:45479600-45481600	Strong transcription	Fetal Stomach	stomach
23	chr1:45479600-45481800	Strong transcription	Primary T cells from cord blood	blood
24	chr1:45479600-45481800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:45479600-45482400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:45479600-45482400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:45479600-45484000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:45479600-45484200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:45479600-45484400	Weak transcription	Right Ventricle	heart
30	chr1:45479800-45481600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:45479800-45481600	Strong transcription	Spleen	Spleen
32	chr1:45479800-45481800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:45479800-45482000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:45479800-45482200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:45479800-45482600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:45480400-45482000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:45480600-45481600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:45480600-45481600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:45480600-45481600	Strong transcription	Hela-S3	cervix
40	chr1:45480600-45481600	Strong transcription	NHDF-Ad	bronchial
41	chr1:45480600-45481800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:45480600-45481800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:45480600-45482000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:45480600-45484200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:45480600-45484200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:45480800-45481600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:45480800-45481600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:45480800-45481600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:45480800-45481600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:45480800-45481600	Strong transcription	Muscle Satellite Cultured Cells	--

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