Variant report

Variant	rs4951639
Chromosome Location	chr1:212975778-212975779
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	MAX	chr1:212975608-212975808	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
2	chr1:212964819..212966751-chr1:212974786..212977581,2	K562	blood:
3	chr1:212974956..212977030-chr1:212986596..212988395,2	K562	blood:

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

Extended variants
information (count: 72 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127613	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1021994	0.87[ASN][1000 genomes]
rs1032962	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1032963	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1032964	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1032965	0.91[ASN][1000 genomes]
rs10746436	0.88[LWK][hapmap];0.96[YRI][hapmap]
rs10779583	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863992	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10864002	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];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10864003	0.96[YRI][hapmap]
rs11120005	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11120028	0.96[ASN][1000 genomes]
rs11120034	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120038	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038225	0.88[ASN][1000 genomes]
rs12124669	0.94[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs12133194	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12239017	0.84[EUR][1000 genomes]
rs12568552	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744555	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];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12757944	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507359	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs15702	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1580991	0.87[EUR][1000 genomes]
rs1580992	0.87[EUR][1000 genomes]
rs1605420	0.83[EUR][1000 genomes]
rs1813705	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1848243	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292214	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2456818	0.92[ASN][1000 genomes]
rs2456827	0.96[ASN][1000 genomes]
rs2456828	0.88[ASN][1000 genomes]
rs2884675	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738800	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3738802	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3949369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4639827	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4951464	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540766	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665489	0.87[EUR][1000 genomes]
rs6670373	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6670869	0.93[EUR][1000 genomes]
rs6678961	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6681851	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685864	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686145	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686164	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6689799	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6694887	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6696870	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696908	0.81[EUR][1000 genomes]
rs6700465	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6702544	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6703982	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7513199	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513210	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513734	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513772	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7514070	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7522100	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7528303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535608	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7538853	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7543603	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7547100	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7555930	0.87[AMR][1000 genomes];0.91[EUR][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	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
2	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
3	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
4	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4951639	NEK2	cis	parietal	SCAN
rs4951639	LQK1	cis	parietal	SCAN
rs4951639	LQK1	cis	cerebellum	SCAN
rs4951639	FLVCR1-AS1	cis	Whole Blood	GTEx
rs4951639	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs4951639	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs4951639	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs4951639	FLVCR1-AS1	cis	lung	GTEx
rs4951639	NCRNA00292	cis	lymphoblastoid	seeQTL
rs4951639	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs4951639	NSL1	cis	lymphoblastoid	seeQTL
rs4951639	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs4951639	TATDN3	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
3	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
5	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
7	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
10	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
11	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
12	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
14	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
16	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
17	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:212967200-212989600	Weak transcription	NHLF	lung
20	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
22	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
23	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
24	chr1:212969000-212976200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:212969000-212976400	Strong transcription	Liver	Liver
26	chr1:212969000-212980000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:212969000-212980000	Strong transcription	Dnd41	blood
28	chr1:212969000-212982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:212969000-212982600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:212969000-212983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:212969200-212976200	Strong transcription	Fetal Thymus	thymus
32	chr1:212969400-212978600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:212969600-212989000	Weak transcription	HepG2	liver
34	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:212970000-212976200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:212970000-212976200	Strong transcription	Adipose Nuclei	Adipose
37	chr1:212970200-212976200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:212970400-212975800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:212970600-212977600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:212970600-212977800	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:212970600-212982800	Weak transcription	Ovary	ovary
42	chr1:212970600-212985200	Weak transcription	Pancreas	Pancrea
43	chr1:212970600-212989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:212971000-212975800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:212971000-212989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:212971200-212977400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:212971200-212979200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:212971200-212983800	Weak transcription	NH-A	brain
49	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:212971400-212987600	Weak transcription	Small Intestine	intestine

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