Variant report

Variant	rs4357530
Chromosome Location	chr1:151103153-151103154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151102270..151104122-chr1:151117546..151119575,3	K562	blood:
2	chr1:151100859..151103920-chr1:151107452..151111935,4	MCF-7	breast:
3	chr1:151099788..151103928-chr1:151106315..151110197,5	K562	blood:
4	chr1:151101938..151104431-chr1:151107566..151109145,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA6C-1	chr1:151102536-151104086	NONHSAT006361
2	lnc-SEMA6C-1	chr1:151102551-151104086	ENSG00000261168.1

No data

Variant related genes	Relation type
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10749659	0.87[ASN][1000 genomes]
rs10788797	0.89[CHB][hapmap]
rs10788798	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10788800	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888405	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204777	0.86[JPT][hapmap]
rs11204779	0.90[ASN][1000 genomes]
rs11204780	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11204782	0.85[JPT][hapmap]
rs11807526	0.86[JPT][hapmap]
rs12087892	0.86[JPT][hapmap]
rs12134957	0.87[ASN][1000 genomes]
rs12569193	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1524773	0.85[JPT][hapmap]
rs15740	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap]
rs2067606	0.86[JPT][hapmap]
rs2091219	0.84[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs2140709	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2864700	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs2902810	0.83[CHD][hapmap]
rs3738481	0.85[JPT][hapmap]
rs3806386	0.83[CHD][hapmap]
rs4360524	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4512652	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4970936	0.85[ASN][1000 genomes]
rs4970941	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs4970991	0.82[CHB][hapmap]
rs4970993	0.86[JPT][hapmap]
rs4970997	0.88[ASN][1000 genomes]
rs4970998	0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4971002	0.81[ASN][1000 genomes]
rs4971005	0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4971006	0.81[ASN][1000 genomes]
rs4971007	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4971008	0.86[JPT][hapmap]
rs61819219	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587552	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.81[MEX][hapmap]
rs6587553	0.83[CHD][hapmap]
rs6656450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674970	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6676190	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691701	0.82[CHB][hapmap]
rs6697617	0.87[ASN][1000 genomes]
rs6702344	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7522608	0.88[ASN][1000 genomes]
rs7523731	0.86[JPT][hapmap]
rs7546304	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554936	0.92[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4357530	MRPS21	cis	cerebellum	SCAN
rs4357530	ZNF687	cis	cerebellum	SCAN
rs4357530	CDC42SE1	cis	Lymphoblastoid	GTEx
rs4357530	LYSMD1	cis	parietal	SCAN
rs4357530	PEX11B	cis	parietal	SCAN
rs4357530	PRPF3	cis	cerebellum	SCAN
rs4357530	LCE3B	cis	parietal	SCAN
rs4357530	LYSMD1	cis	cerebellum	SCAN
rs4357530	GABPB2	cis	cerebellum	SCAN
rs4357530	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs4357530	CDC42SE1	cis	lymphoblastoid	seeQTL
rs4357530	CDC42SE1	cis	parietal	SCAN
rs4357530	BNIPL	cis	lung	GTEx
rs4357530	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
2	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon
4	chr1:151067000-151103400	Weak transcription	Fetal Brain Male	brain
5	chr1:151079800-151103400	Weak transcription	NH-A	brain
6	chr1:151079800-151103400	Weak transcription	NHEK	skin
7	chr1:151079800-151103400	Weak transcription	NHLF	lung
8	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
9	chr1:151079800-151114800	Weak transcription	HSMM	muscle
10	chr1:151081200-151103400	Weak transcription	GM12878-XiMat	blood
11	chr1:151083400-151103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:151085800-151103200	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:151087000-151103600	Weak transcription	Psoas Muscle	Psoas
14	chr1:151089200-151103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:151090800-151103200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:151090800-151103400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:151090800-151103400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:151090800-151103400	Weak transcription	Ovary	ovary
19	chr1:151090800-151103600	Weak transcription	Esophagus	oesophagus
20	chr1:151090800-151105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:151091200-151103800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:151091600-151103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:151091600-151103200	Weak transcription	Fetal Lung	lung
24	chr1:151091600-151103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:151091800-151103200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:151091800-151103200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:151091800-151103200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:151091800-151103400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:151091800-151103400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:151091800-151103400	Weak transcription	Fetal Brain Female	brain
31	chr1:151091800-151103400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:151091800-151103400	Weak transcription	Spleen	Spleen
33	chr1:151091800-151103600	Weak transcription	Gastric	stomach
34	chr1:151091800-151103600	Weak transcription	Lung	lung
35	chr1:151091800-151103600	Weak transcription	Pancreas	Pancrea
36	chr1:151091800-151103600	Weak transcription	Right Ventricle	heart
37	chr1:151092000-151103400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:151092200-151103200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:151092800-151103600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:151093000-151103200	Weak transcription	Fetal Stomach	stomach
41	chr1:151094600-151103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:151095000-151103600	Weak transcription	Liver	Liver
43	chr1:151095200-151103400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:151095200-151103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:151095200-151103400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:151095400-151103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:151095600-151103400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:151095600-151103600	Weak transcription	Brain Substantia Nigra	brain
49	chr1:151095800-151103400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:151095800-151103400	Weak transcription	Left Ventricle	heart

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