Variant report

Variant	rs6678729
Chromosome Location	chr1:45210329-45210330
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	chr1:45209761-45210650	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45207667..45210587-chr1:45241224..45243801,2	MCF-7	breast:

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000264294	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000225721	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10127448	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465818	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211030	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211031	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211034	0.90[ASN][1000 genomes]
rs11584031	0.85[ASN][1000 genomes]
rs11801067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808189	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808852	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094028	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117881	0.83[ASN][1000 genomes]
rs12136048	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136099	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410588	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12742914	0.90[ASN][1000 genomes]
rs16832228	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4542248	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6429548	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6656337	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658470	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671255	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685176	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688710	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698847	0.81[AMR][1000 genomes]
rs7512710	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518836	0.93[ASN][1000 genomes]
rs7524446	0.89[EUR][1000 genomes]
rs7536146	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550170	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555065	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9988580	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45223400	Weak transcription	Lung	lung
3	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
4	chr1:45206200-45213400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:45206200-45218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:45206200-45220000	Weak transcription	Spleen	Spleen
8	chr1:45206200-45224800	Weak transcription	Esophagus	oesophagus
9	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
10	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
11	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
14	chr1:45206400-45211800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:45206400-45212000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:45206400-45213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:45206400-45213400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:45206400-45218400	Weak transcription	Gastric	stomach
19	chr1:45206400-45218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:45206400-45218600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:45206400-45219000	Weak transcription	Primary B cells from cord blood	blood
22	chr1:45206400-45219600	Weak transcription	Placenta	Placenta
23	chr1:45206400-45221400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:45206600-45211600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:45206600-45213000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:45206600-45213400	Weak transcription	Fetal Brain Female	brain
29	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:45206800-45210800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:45206800-45211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:45206800-45223000	Weak transcription	Fetal Kidney	kidney
33	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
34	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:45207000-45211800	Weak transcription	Fetal Lung	lung
36	chr1:45207000-45216000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:45207000-45218800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:45207200-45210400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:45207400-45210400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:45208200-45212000	Strong transcription	Fetal Thymus	thymus
47	chr1:45208400-45210400	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:45208400-45210600	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:45208400-45210600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:45208400-45210800	Strong transcription	Thymus	Thymus

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