Variant report

Variant	rs6463540
Chromosome Location	chr7:6296843-6296844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6280841..6283704-chr7:6294906..6297324,2	K562	blood:
2	chr7:6290547..6293891-chr7:6295729..6298569,3	MCF-7	breast:
3	chr7:6295108..6297565-chr7:6362435..6365344,2	MCF-7	breast:
4	chr7:6295150..6302020-chr7:6308719..6313384,10	MCF-7	breast:
5	chr7:6295146..6297854-chr7:6301609..6304566,2	MCF-7	breast:
6	chr7:6295902..6297689-chr7:6310840..6312343,2	MCF-7	breast:
7	chr7:6289334..6292556-chr7:6296327..6298930,3	K562	blood:

Variant related genes	Relation type
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10046499	1.00[JPT][hapmap]
rs10224504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10225119	1.00[JPT][hapmap]
rs10240510	1.00[JPT][hapmap]
rs10241174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10241580	0.95[ASN][1000 genomes]
rs10244640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10245186	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10247585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10252947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10253501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10255662	0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10255914	1.00[JPT][hapmap]
rs10261217	1.00[JPT][hapmap]
rs10263878	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10267982	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10268916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs10270609	0.87[EUR][1000 genomes]
rs10275021	1.00[JPT][hapmap]
rs10279137	1.00[JPT][hapmap]
rs10280585	1.00[JPT][hapmap]
rs11768047	1.00[JPT][hapmap]
rs11768749	1.00[JPT][hapmap]
rs11976961	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12667392	1.00[JPT][hapmap]
rs13437890	1.00[JPT][hapmap]
rs17136048	1.00[JPT][hapmap]
rs34073302	0.82[EUR][1000 genomes]
rs34312608	0.90[EUR][1000 genomes]
rs34904930	0.82[EUR][1000 genomes]
rs34939060	0.93[EUR][1000 genomes]
rs35257722	0.92[EUR][1000 genomes]
rs35372475	0.82[EUR][1000 genomes]
rs35402521	0.92[EUR][1000 genomes]
rs35868999	0.92[EUR][1000 genomes]
rs35882223	0.92[EUR][1000 genomes]
rs35934233	0.82[EUR][1000 genomes]
rs59180903	1.00[ASN][1000 genomes]
rs6463535	0.97[EUR][1000 genomes]
rs6463541	1.00[JPT][hapmap]
rs6463544	1.00[JPT][hapmap]
rs6942707	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6944071	1.00[JPT][hapmap]
rs6944216	1.00[ASN][1000 genomes]
rs6946205	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6949823	1.00[JPT][hapmap]
rs6955065	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6960965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6961095	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6962767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6969814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6969863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71531366	0.92[EUR][1000 genomes]
rs71531367	0.92[EUR][1000 genomes]
rs71531368	0.92[EUR][1000 genomes]
rs71531370	0.92[EUR][1000 genomes]
rs71531372	0.82[EUR][1000 genomes]
rs71549618	0.82[EUR][1000 genomes]
rs7777433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7780269	1.00[JPT][hapmap]
rs7780702	0.84[EUR][1000 genomes]
rs7783018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7783827	0.84[EUR][1000 genomes]
rs7784025	0.95[ASN][1000 genomes]
rs7791225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800777	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7807841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs886675	0.90[YRI][hapmap]
rs958329	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
7	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	64 gene(s)	inside rSNPs	diseases
10	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6463540	PSCD3	Cis_1M	lymphoblastoid	RTeQTL
rs6463540	CYTH3	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6287000-6297400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr7:6288200-6310400	Weak transcription	Brain Angular Gyrus	brain
3	chr7:6288400-6297400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:6288400-6297400	Weak transcription	Ovary	ovary
5	chr7:6288400-6298400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:6288400-6300000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:6288400-6306600	Weak transcription	Esophagus	oesophagus
8	chr7:6289200-6297400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:6289200-6300000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:6289400-6297200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:6291600-6297400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:6292400-6300000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:6293000-6306400	Weak transcription	NHEK	skin
14	chr7:6293400-6306600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:6293600-6298200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr7:6293600-6299000	Enhancers	HSMMtube	muscle
17	chr7:6293800-6299000	Enhancers	HSMM	muscle
18	chr7:6293800-6299200	Enhancers	Stomach Mucosa	stomach
19	chr7:6294200-6297600	Enhancers	HepG2	liver
20	chr7:6294200-6303200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:6294400-6300600	Enhancers	A549	lung
22	chr7:6294400-6301200	Enhancers	Adipose Nuclei	Adipose
23	chr7:6294800-6298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:6295000-6298400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr7:6295200-6298200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:6295200-6299200	Enhancers	Primary hematopoietic stem cells	blood
27	chr7:6295200-6300200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:6295600-6298200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:6295600-6298800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr7:6295600-6299000	Flanking Active TSS	GM12878-XiMat	blood
31	chr7:6295800-6297600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:6295800-6297800	Enhancers	Fetal Heart	heart
33	chr7:6295800-6298000	Enhancers	Rectal Smooth Muscle	rectum
34	chr7:6295800-6298400	Enhancers	Fetal Intestine Large	intestine
35	chr7:6295800-6298400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:6295800-6299200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr7:6295800-6299400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:6296000-6297000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr7:6296000-6299000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr7:6296000-6299000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr7:6296000-6299000	Enhancers	Dnd41	blood
42	chr7:6296000-6300800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:6296200-6297000	Enhancers	Primary T cells from cord blood	blood
44	chr7:6296200-6297000	Enhancers	Liver	Liver
45	chr7:6296200-6297400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr7:6296200-6297400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:6296200-6298400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr7:6296200-6299200	Enhancers	Primary B cells from peripheral blood	blood
49	chr7:6296200-6299200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:6296400-6297000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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