Variant report

Variant	rs6938640
Chromosome Location	chr6:2040226-2040227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1609442..1611153-chr6:2038341..2040817,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11242731	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206139	0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212324	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13218855	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1802	0.83[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1969667	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2076916	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2875725	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35546016	0.80[ASN][1000 genomes]
rs4959164	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959620	0.80[ASN][1000 genomes]
rs4959629	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959632	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs501038	0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs538391	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs635234	0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6596868	0.83[EUR][1000 genomes]
rs668674	0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6909371	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6910252	0.91[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6922565	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751738	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs7771247	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs7772545	0.83[JPT][hapmap]
rs9328080	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9378669	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9391942	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9392351	0.91[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9392366	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs9405537	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9405545	0.84[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9503076	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9503080	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	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
7	nsv981098	chr6:2008599-2102267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv527735	chr6:2028237-2097654	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2022400-2042800	Weak transcription	Right Atrium	heart
2	chr6:2022400-2055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:2022400-2080600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:2029800-2040400	Weak transcription	Stomach Mucosa	stomach
5	chr6:2030000-2053600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:2031800-2041800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:2032600-2043400	Weak transcription	HSMM	muscle
8	chr6:2034200-2044400	Weak transcription	Primary B cells from cord blood	blood
9	chr6:2035600-2052600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:2037000-2043800	Enhancers	Fetal Thymus	thymus
11	chr6:2038600-2043800	Enhancers	Thymus	Thymus
12	chr6:2038800-2041200	Enhancers	Primary T cells from cord blood	blood
13	chr6:2039000-2044200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:2039400-2040400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:2039400-2041200	Enhancers	Dnd41	blood
16	chr6:2039400-2052600	Weak transcription	HepG2	liver
17	chr6:2039600-2040400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:2039600-2040600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:2039600-2040600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:2040200-2040600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:2040200-2040600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:2040200-2040600	Enhancers	Primary T helper cells fromperipheralblood	blood

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