Variant report

Variant	rs6702555
Chromosome Location	chr1:225663433-225663434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
2	chr1:225661061..225665257-chr1:226163112..226166318,3	K562	blood:
3	chr1:225662226..225663837-chr1:226162713..226165257,2	K562	blood:
4	chr1:225662746..225665144-chr1:225672666..225674544,2	MCF-7	breast:
5	chr1:225662326..225663674-chr1:226098265..226099949,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243709	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10753406	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799311	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799313	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10799314	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799315	0.81[AFR][1000 genomes]
rs10799316	0.89[ASN][1000 genomes]
rs10799317	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799318	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799319	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915828	0.84[ASN][1000 genomes]
rs10915830	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10915833	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10915834	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915835	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10915837	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10915838	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10915839	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915847	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11584675	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12028305	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222440	0.91[ASN][1000 genomes]
rs12729655	0.85[ASN][1000 genomes]
rs2840958	0.80[EUR][1000 genomes]
rs3820226	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3856156	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653639	0.85[ASN][1000 genomes]
rs4653643	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476540	0.81[EUR][1000 genomes]
rs487591	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs498350	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs510293	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs511649	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs516249	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs551996	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554744	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554992	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561656	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576861	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6426076	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426077	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6426078	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6668770	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6676201	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6678806	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6697783	0.81[ASN][1000 genomes]
rs6702538	0.81[ASN][1000 genomes]
rs6751	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712062	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515907	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7515939	0.81[ASN][1000 genomes]
rs7515963	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7524766	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540181	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7541598	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7555139	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555553	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947034	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9804142	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv873227	chr1:225656388-225687981	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv8880	chr1:225656408-225687710	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv826842	chr1:225658062-225686586	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv441740	chr1:225659217-225684196	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6702555	LBR	cis	Artery Tibial	GTEx
rs6702555	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
2	chr1:225660600-225666200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:225660800-225666200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:225660800-225666200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:225660800-225666800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:225661000-225666200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:225661000-225666200	Enhancers	Fetal Thymus	thymus
8	chr1:225661600-225663800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:225662000-225667000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:225662200-225671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:225662400-225663600	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:225662400-225665000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:225662600-225671800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:225663000-225665400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:225663200-225664000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:225663200-225664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:225663200-225664200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:225663200-225664200	Weak transcription	NHDF-Ad	bronchial
19	chr1:225663200-225664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:225663200-225665000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:225663200-225665200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:225663200-225665400	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:225663200-225665400	Weak transcription	NHEK	skin
24	chr1:225663200-225665600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:225663200-225665600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:225663200-225665600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:225663200-225665600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:225663200-225665600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:225663200-225665600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:225663200-225665600	Weak transcription	Fetal Stomach	stomach
31	chr1:225663200-225665600	Weak transcription	Spleen	Spleen
32	chr1:225663200-225665600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:225663200-225665800	Weak transcription	HSMMtube	muscle
34	chr1:225663200-225666200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:225663200-225668600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:225663200-225668600	Weak transcription	Pancreas	Pancrea
37	chr1:225663200-225668600	Weak transcription	Stomach Mucosa	stomach
38	chr1:225663200-225668800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:225663200-225668800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:225663200-225669800	Weak transcription	Ovary	ovary
41	chr1:225663200-225670200	Weak transcription	Osteobl	bone
42	chr1:225663200-225683800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:225663200-225686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:225663400-225663600	Bivalent/Poised TSS	HepG2	liver
46	chr1:225663400-225663800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:225663400-225663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:225663400-225663800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:225663400-225663800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:225663400-225665200	Weak transcription	Primary B cells from cord blood	blood

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