Variant report

Variant	rs4959632
Chromosome Location	chr6:2105977-2105978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1610117..1612459-chr6:2103517..2106482,4	MCF-7	breast:
2	chr6:2040678..2043654-chr6:2103622..2106281,2	MCF-7	breast:
3	chr6:1612494..1615565-chr6:2103145..2107069,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12212324	0.82[CEU][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs13218855	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1802	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1969667	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1969668	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076916	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]
rs2875725	0.80[EUR][1000 genomes]
rs3800156	0.85[MEX][hapmap]
rs4959164	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4959620	0.82[CHB][hapmap]
rs4959629	0.82[EUR][1000 genomes]
rs501038	0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs538391	0.87[ASN][1000 genomes]
rs635234	0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs668674	0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6909371	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6910252	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6922565	0.80[EUR][1000 genomes]
rs6938640	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7751738	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs7771247	0.81[CEU][hapmap]
rs9378669	0.81[EUR][1000 genomes]
rs9391942	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9392351	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9392366	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9405537	0.81[EUR][1000 genomes]
rs9405545	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9503076	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9503080	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.85[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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv522608	chr6:2032259-2203888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1019227	chr6:2038843-2142395	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv538097	chr6:2038843-2142395	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
10	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
11	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
12	nsv883387	chr6:2086679-2176239	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
14	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
15	nsv519587	chr6:2097654-2145447	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4959632	MYLK4	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2065000-2117400	Weak transcription	Pancreas	Pancrea
2	chr6:2079000-2108800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:2081000-2108800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:2081200-2113000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:2081600-2131800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:2082800-2109000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:2088800-2112200	Weak transcription	Small Intestine	intestine
8	chr6:2099400-2109200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:2104400-2109000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:2104400-2132000	Weak transcription	Fetal Intestine Large	intestine
11	chr6:2104600-2108800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:2104600-2108800	Weak transcription	HepG2	liver
13	chr6:2104600-2109000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:2104600-2109000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:2104600-2110000	Weak transcription	Osteobl	bone
16	chr6:2104600-2110800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:2104600-2111000	Weak transcription	Hela-S3	cervix
18	chr6:2104600-2111200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:2104600-2111200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:2104600-2111200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:2104600-2112000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:2104600-2116600	Weak transcription	Dnd41	blood
23	chr6:2104600-2128200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:2104800-2109000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:2104800-2110200	Weak transcription	HUVEC	blood vessel
26	chr6:2104800-2112200	Weak transcription	Left Ventricle	heart
27	chr6:2105000-2109200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:2105200-2123400	Weak transcription	Gastric	stomach

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