Variant report

Variant	rs3750612
Chromosome Location	chr10:99517355-99517356
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	chr10:99517271-99517662	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:99515749-99517695	K562	blood:	n/a	n/a
3	POLR2A	chr10:99516780-99517365	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ZFYVE27	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10748708	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10748709	0.86[ASN][1000 genomes]
rs10786367	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs10786370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10786371	0.82[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10786372	0.83[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10786373	0.84[ASN][1000 genomes]
rs10882993	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10882995	0.89[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10882996	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10882997	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10882998	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11189352	0.83[ASN][1000 genomes]
rs11189353	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11189355	0.89[CEU][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11189356	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11189357	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11189359	0.89[CEU][hapmap];0.82[CHD][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11189360	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11189361	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11189362	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189374	0.80[AMR][1000 genomes]
rs11591898	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12412543	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12569711	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12783992	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1538723	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1556971	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1981237	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1981238	0.94[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2010732	0.81[ASN][1000 genomes]
rs2027376	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2039826	0.94[CEU][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34283185	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3750614	0.85[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3750615	0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3814558	0.85[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3814559	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814560	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4244329	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4244330	0.81[AMR][1000 genomes]
rs4917784	0.83[JPT][hapmap]
rs4917786	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4919139	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs7072751	0.86[ASN][1000 genomes]
rs7077725	0.82[ASN][1000 genomes]
rs7080894	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs7080953	0.88[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7081361	0.83[AMR][1000 genomes]
rs7081652	0.88[ASN][1000 genomes]
rs7094519	0.81[ASN][1000 genomes]
rs7099540	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs7100453	0.80[AMR][1000 genomes]
rs7478323	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7907679	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7910589	0.86[ASN][1000 genomes]
rs7916164	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7916454	0.85[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7916593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7922907	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883324	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946777	0.85[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs946778	0.85[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99498400-99517600	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
5	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr10:99498600-99517800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
9	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:99498600-99520600	Strong transcription	Osteobl	bone
11	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
15	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
17	chr10:99498800-99522400	Strong transcription	Dnd41	blood
18	chr10:99499000-99517800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:99499000-99518000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:99499200-99518000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr10:99499400-99519000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:99499600-99519200	Strong transcription	Placenta	Placenta
27	chr10:99499800-99518000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr10:99500000-99523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:99500200-99518000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:99500400-99522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:99500600-99523200	Strong transcription	Brain Germinal Matrix	brain
32	chr10:99500800-99517800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:99500800-99518800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:99501200-99517600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr10:99502000-99517600	Strong transcription	Rectal Smooth Muscle	rectum
36	chr10:99502000-99517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:99502000-99517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr10:99502000-99518000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:99502000-99522800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr10:99502200-99522600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr10:99502400-99520000	Strong transcription	Primary B cells from cord blood	blood
42	chr10:99502600-99517800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:99502600-99518000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:99502600-99519200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:99502600-99522600	Strong transcription	Primary T cells from cord blood	blood
46	chr10:99502800-99518000	Strong transcription	A549	lung
47	chr10:99502800-99521600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:99502800-99522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr10:99503000-99524000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:99503200-99519000	Strong transcription	Primary T cells fromperipheralblood	blood

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