Variant report

Variant	rs3738800
Chromosome Location	chr1:212960866-212960867
allele	A/G
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:6)
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	STAT3	chr1:212960768-212961054	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212781016..212783376-chr1:212959692..212961449,2	MCF-7	breast:
2	chr1:212960294..212962883-chr1:213188555..213191323,2	K562	blood:
3	chr1:212955485..212957431-chr1:212958159..212961189,3	K562	blood:
4	chr1:212958137..212960134-chr1:212960164..212962206,2	K562	blood:
5	chr1:212949377..212951315-chr1:212960542..212962942,2	K562	blood:
6	chr1:212958789..212962181-chr1:212964353..212966610,4	K562	blood:

No data

Variant related genes	Relation type
TATDN3	TF binding region
ENSG00000174606	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1021994	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1032962	0.87[ASN][1000 genomes]
rs1032963	0.88[ASN][1000 genomes]
rs1032965	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10779583	0.95[ASN][1000 genomes]
rs10864002	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11120028	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120034	0.89[ASN][1000 genomes]
rs11120038	0.88[ASN][1000 genomes]
rs12038225	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12124669	0.81[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs12133194	0.88[ASN][1000 genomes]
rs12568552	0.96[ASN][1000 genomes]
rs12744555	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12757944	0.89[ASN][1000 genomes]
rs1813705	0.99[ASN][1000 genomes]
rs2456818	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2456827	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2456828	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2492779	1.00[YRI][hapmap]
rs2492784	0.94[AFR][1000 genomes]
rs2884675	0.89[ASN][1000 genomes]
rs3949369	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4951464	0.90[ASN][1000 genomes]
rs4951639	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6540766	0.96[ASN][1000 genomes]
rs6540767	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6681851	0.88[ASN][1000 genomes]
rs6685864	0.88[ASN][1000 genomes]
rs6686145	0.88[ASN][1000 genomes]
rs6689799	0.88[ASN][1000 genomes]
rs6696870	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7528303	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3738800	LQK1	cis	cerebellum	SCAN
rs3738800	NSL1	cis	lymphoblastoid	seeQTL
rs3738800	BATF3	cis	lymphoblastoid	seeQTL
rs3738800	FLVCR1	cis	Thyroid	GTEx
rs3738800	FLVCR1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212923800-212964200	Weak transcription	HMEC	breast
6	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
8	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
10	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
11	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
12	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
16	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
20	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:212953800-212961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:212954000-212961000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:212954000-212961000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212954000-212961000	Strong transcription	Liver	Liver
26	chr1:212954000-212961000	Strong transcription	Fetal Thymus	thymus
27	chr1:212954000-212961200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:212954000-212961200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:212954200-212961000	Strong transcription	Dnd41	blood
30	chr1:212954200-212961600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
32	chr1:212954800-212961000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:212955000-212961000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:212955000-212961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:212955000-212961600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:212955000-212962000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:212955000-212964200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:212955200-212961600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:212955200-212963000	Weak transcription	Brain Germinal Matrix	brain
40	chr1:212955600-212961800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:212955600-212964200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:212955800-212964400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:212956000-212961800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:212956400-212961000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:212956400-212961000	Strong transcription	Hela-S3	cervix
46	chr1:212956400-212962000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:212956400-212963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:212956400-212964200	Weak transcription	NHLF	lung
49	chr1:212956600-212962000	Weak transcription	GM12878-XiMat	blood
50	chr1:212956600-212963800	Weak transcription	NHDF-Ad	bronchial

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