Variant report

Variant	rs3753650
Chromosome Location	chr1:225964342-225964343
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:225963858-225966969	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
2	chr1:225964211..225968767-chr1:226248453..226252378,4	K562	blood:
3	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
4	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
5	chr1:225963873..225967033-chr1:226031330..226035962,4	MCF-7	breast:
6	chr1:225963989..225965773-chr1:226185779..226187510,2	K562	blood:
7	chr1:225961838..225964716-chr1:226068822..226070788,2	K562	blood:
8	chr1:225963779..225965569-chr1:226150173..226152058,2	MCF-7	breast:
9	chr1:225964273..225967291-chr1:226184778..226188048,4	K562	blood:
10	chr1:225963673..225968224-chr1:226032543..226034938,4	MCF-7	breast:
11	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
12	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
13	chr1:225964257..225969087-chr1:226030786..226035881,7	K562	blood:
14	chr1:225959006..225964473-chr1:225964619..225968366,9	MCF-7	breast:
15	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:

No data

Variant related genes	Relation type
SRP9	TF binding region
ENSG00000143751	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000143819	Chromatin interaction
ENSG00000154380	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000242861	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000213032	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes]
rs10915871	1.00[AFR][1000 genomes]
rs10915872	1.00[AFR][1000 genomes]
rs10915874	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10915875	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12021669	1.00[AFR][1000 genomes]
rs12021809	1.00[AFR][1000 genomes]
rs12023203	1.00[AFR][1000 genomes]
rs12025075	1.00[AFR][1000 genomes]
rs12025085	1.00[AFR][1000 genomes]
rs12025267	1.00[AFR][1000 genomes]
rs12026657	1.00[AFR][1000 genomes]
rs12029847	1.00[AFR][1000 genomes]
rs12031637	1.00[AFR][1000 genomes]
rs12032511	1.00[AFR][1000 genomes]
rs12034342	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12038476	1.00[AFR][1000 genomes]
rs12039184	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047520	1.00[AFR][1000 genomes]
rs12048908	1.00[AFR][1000 genomes]
rs12562612	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1849685	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2078389	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738035	1.00[AFR][1000 genomes]
rs4557929	1.00[AFR][1000 genomes]
rs61849043	1.00[AFR][1000 genomes]
rs61849046	1.00[AFR][1000 genomes]
rs61849047	1.00[AFR][1000 genomes]
rs61851667	1.00[AFR][1000 genomes]
rs716966	1.00[AFR][1000 genomes];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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225952200-225964400	Weak transcription	Fetal Brain Female	brain
2	chr1:225952200-225965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225954800-225964400	Weak transcription	Small Intestine	intestine
4	chr1:225956800-225964600	Weak transcription	Right Ventricle	heart
5	chr1:225957000-225965000	Weak transcription	Gastric	stomach
6	chr1:225958600-225964800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:225959200-225964600	Weak transcription	Psoas Muscle	Psoas
8	chr1:225959200-225964800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:225959600-225964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:225959600-225964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:225959800-225964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:225960000-225964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:225960000-225964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:225960200-225964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:225960200-225964800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:225960400-225964400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:225960400-225964400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:225960400-225964400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:225960400-225964400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:225960400-225964400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:225960400-225964400	Weak transcription	HUVEC	blood vessel
22	chr1:225960400-225964400	Weak transcription	NHDF-Ad	bronchial
23	chr1:225960400-225964600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:225960400-225965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:225960600-225964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:225960600-225964600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:225960600-225964600	Weak transcription	Fetal Brain Male	brain
28	chr1:225960600-225964600	Weak transcription	Fetal Heart	heart
29	chr1:225960600-225964800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:225960800-225964400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:225960800-225964400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:225960800-225964400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:225960800-225964400	Weak transcription	Adipose Nuclei	Adipose
34	chr1:225960800-225964400	Weak transcription	Liver	Liver
35	chr1:225960800-225964400	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:225960800-225964400	Weak transcription	Fetal Kidney	kidney
37	chr1:225960800-225964400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:225960800-225964400	Weak transcription	NHLF	lung
39	chr1:225960800-225964600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:225960800-225964600	Enhancers	Colon Smooth Muscle	Colon
41	chr1:225960800-225964600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:225960800-225964600	Weak transcription	Right Atrium	heart
43	chr1:225960800-225964800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:225960800-225964800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:225960800-225964800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:225960800-225964800	Weak transcription	Colonic Mucosa	Colon
47	chr1:225960800-225964800	Weak transcription	Left Ventricle	heart
48	chr1:225960800-225964800	Weak transcription	Ovary	ovary
49	chr1:225961000-225964400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:225961000-225964400	Weak transcription	Brain Anterior Caudate	brain

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