Variant report

Variant	rs913499
Chromosome Location	chr6:37038432-37038433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37038083..37040728-chr6:37067671..37070819,3	MCF-7	breast:
2	chr6:37025397..37029627-chr6:37037607..37042418,9	MCF-7	breast:
3	chr6:37037124..37041765-chr6:37137125..37140593,5	MCF-7	breast:
4	chr6:37038270..37040946-chr6:37102202..37104279,3	MCF-7	breast:
5	chr6:37036808..37040698-chr6:37041272..37044112,3	MCF-7	breast:
6	chr6:37014703..37016638-chr6:37036621..37038696,2	K562	blood:

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10223714	0.90[ASN][1000 genomes]
rs1224487	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1224488	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1224491	0.83[ASN][1000 genomes]
rs1228575	0.85[ASN][1000 genomes]
rs1724094	0.83[ASN][1000 genomes]
rs1753301	0.85[ASN][1000 genomes]
rs2025998	0.85[ASN][1000 genomes]
rs2094575	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2149336	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4317401	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs4711482	0.85[ASN][1000 genomes]
rs4711483	0.85[ASN][1000 genomes]
rs4714034	0.85[CEU][hapmap]
rs6457974	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs6457976	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457978	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457979	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457980	0.85[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs6924660	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6934536	0.88[JPT][hapmap]
rs6939869	0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7748291	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750403	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7750614	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7750717	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7751821	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7770544	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7774073	0.88[ASN][1000 genomes]
rs831484	0.85[ASN][1000 genomes]
rs831487	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs831489	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs831491	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs831497	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs831499	0.82[ASN][1000 genomes]
rs831500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs831502	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913500	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs9296207	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9296208	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366927	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9380637	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394401	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394402	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394403	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462258	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470469	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs913499	C6orf130	cis	parietal	SCAN
rs913499	FGD2	cis	multi-tissue	Pritchard
rs913499	PIM1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37028200-37039200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:37028200-37039400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:37028400-37039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:37029600-37039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:37030400-37039600	Weak transcription	A549	lung
6	chr6:37032800-37039200	Weak transcription	K562	blood
7	chr6:37036400-37039200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:37036400-37039400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:37036400-37039600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:37036600-37041800	Weak transcription	Right Atrium	heart
11	chr6:37036800-37039000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:37036800-37039000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:37036800-37039400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:37036800-37041400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:37037000-37039600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:37037000-37041600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:37037200-37039000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:37037200-37039000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:37037200-37039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:37037200-37039200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:37037200-37042800	Enhancers	HepG2	liver
22	chr6:37037200-37045200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:37037400-37039400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:37037400-37039400	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:37037400-37039800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:37037600-37039200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:37037600-37045400	Weak transcription	Spleen	Spleen
28	chr6:37037800-37039200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:37038000-37039400	Weak transcription	Primary B cells from cord blood	blood
30	chr6:37038200-37041200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:37038400-37038600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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