Variant report

Variant	rs3935419
Chromosome Location	chr1:154131870-154131871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154131824-154133751	PFSK-1	brain:	n/a	n/a
2	KAP1	chr1:154131398-154132982	K562	blood:	n/a	n/a
3	POLR2A	chr1:154131566-154132485	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:154130109-154133877	A549	lung:	n/a	n/a
5	JUN	chr1:154129565-154132628	K562	blood:	n/a	chr1:154130854-154130866
6	CBX3	chr1:154131615-154132468	K562	blood:	n/a	n/a
7	POLR2A	chr1:154131748-154132421	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:154131668-154131926	HUVEC	blood vessel:	n/a	n/a
9	CBX3	chr1:154129775-154132565	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153961678..153964688-chr1:154130788..154133613,4	K562	blood:
2	chr1:154128396..154132314-chr1:154154377..154157554,5	MCF-7	breast:
3	chr1:154130730..154134343-chr1:154138562..154143289,5	K562	blood:
4	chr1:154130461..154134364-chr1:154154603..154156791,6	K562	blood:
5	chr1:154130385..154131927-chr1:154191683..154194863,3	K562	blood:
6	chr1:154131512..154133730-chr1:154137495..154140400,2	MCF-7	breast:
7	chr1:154130378..154132866-chr1:154153515..154156872,4	K562	blood:
8	chr1:154111988..154114382-chr1:154131555..154133163,2	MCF-7	breast:
9	chr1:154128722..154131890-chr1:154192091..154194653,3	K562	blood:

No data

Variant related genes	Relation type
NUP210L	TF binding region
ENSG00000264384	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158820	0.91[JPT][hapmap]
rs1044013	0.91[JPT][hapmap]
rs1113142	0.84[YRI][hapmap]
rs11265238	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11265251	0.91[JPT][hapmap]
rs11265425	0.95[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1194593	0.91[JPT][hapmap]
rs1194594	0.92[YRI][hapmap]
rs1194596	0.91[JPT][hapmap]
rs1194597	0.82[YRI][hapmap]
rs1194601	0.91[YRI][hapmap]
rs1194605	0.87[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs12026177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026615	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12028949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038362	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.91[JPT][hapmap]
rs16835846	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1685625	0.80[YRI][hapmap]
rs1760802	0.91[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs2340473	0.86[JPT][hapmap]
rs2500222	0.91[YRI][hapmap]
rs2633434	0.95[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs28372838	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2879788	0.91[JPT][hapmap]
rs3002660	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34128679	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34335016	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35761479	0.87[EUR][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs3790613	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs3811453	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs3811455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3828077	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs4433384	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs4620534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60282844	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427509	0.91[JPT][hapmap]
rs6666943	0.84[YRI][hapmap]
rs6673752	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs6676022	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6719	0.91[JPT][hapmap]
rs715737	0.84[YRI][hapmap]
rs9803857	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3935419	DENND4B	cis	parietal	SCAN
rs3935419	RAB13	cis	parietal	SCAN
rs3935419	HAX1	cis	lymphoblastoid	seeQTL
rs3935419	HAX1	cis	cerebellum	SCAN
rs3935419	HAX1	cis	parietal	SCAN
rs3935419	PIP5K1A	cis	cerebellum	SCAN
rs3935419	SLC27A3	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154126400-154133000	Weak transcription	Ovary	ovary
3	chr1:154126400-154146000	Strong transcription	HMEC	breast
4	chr1:154127000-154143400	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr1:154127000-154143600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:154127000-154148400	Strong transcription	Fetal Intestine Large	intestine
7	chr1:154127000-154149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:154127200-154132400	Genic enhancers	Fetal Thymus	thymus
9	chr1:154127200-154146000	Strong transcription	Fetal Brain Female	brain
10	chr1:154127400-154132800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:154127400-154148200	Strong transcription	Liver	Liver
12	chr1:154127600-154136400	Weak transcription	Right Ventricle	heart
13	chr1:154127600-154136600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:154127600-154136600	Weak transcription	Esophagus	oesophagus
15	chr1:154127600-154148400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:154127800-154140200	Weak transcription	Pancreas	Pancrea
17	chr1:154127800-154150000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:154128000-154134000	Strong transcription	NHDF-Ad	bronchial
19	chr1:154128000-154148400	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:154128000-154150400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:154128000-154150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:154128200-154132000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:154128200-154150200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:154128200-154151200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:154128400-154137200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:154128400-154137800	Weak transcription	Fetal Heart	heart
27	chr1:154128400-154146000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:154128400-154148400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:154128600-154146000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:154128600-154148600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:154129000-154133600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr1:154129200-154133200	Genic enhancers	Thymus	Thymus
33	chr1:154129400-154134000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:154129600-154132000	Enhancers	Stomach Mucosa	stomach
35	chr1:154129600-154133600	Genic enhancers	Dnd41	blood
36	chr1:154129600-154143600	Strong transcription	HSMMtube	muscle
37	chr1:154129600-154145600	Strong transcription	HepG2	liver
38	chr1:154129600-154145600	Strong transcription	NHEK	skin
39	chr1:154129600-154149800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:154129600-154150400	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr1:154129800-154132000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:154129800-154133600	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:154129800-154148200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:154130000-154132200	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr1:154130000-154133200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:154130000-154133800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:154130000-154134000	Strong transcription	Brain Germinal Matrix	brain
48	chr1:154130000-154135000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:154130000-154148400	Strong transcription	HSMM	muscle
50	chr1:154130200-154132000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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