Variant report

Variant	rs6910715
Chromosome Location	chr6:37776962-37776963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37756505..37762867-chr6:37772774..37778127,6	MCF-7	breast:
2	chr6:37773348..37778942-chr6:37784434..37789284,15	MCF-7	breast:
3	chr6:37775388..37777392-chr6:37792232..37794017,2	MCF-7	breast:
4	chr6:37771553..37779758-chr6:37784024..37789413,23	MCF-7	breast:
5	chr6:37770736..37773178-chr6:37775480..37777364,3	K562	blood:
6	chr6:37773868..37777488-chr6:37778348..37782159,4	K562	blood:
7	chr6:37770736..37773178-chr6:37775480..37777289,2	K562	blood:

Variant related genes	Relation type
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10428769	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10485030	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10947702	0.89[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10947704	1.00[CEU][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11751781	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11751927	0.82[EUR][1000 genomes]
rs11751962	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11752521	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11752809	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11752814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11753300	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11755095	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11755629	1.00[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11756713	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11757161	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11759458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11759496	0.87[EUR][1000 genomes]
rs11759826	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11964613	0.82[JPT][hapmap]
rs11964671	0.82[JPT][hapmap]
rs11967129	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11969988	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11970017	0.82[JPT][hapmap]
rs12660919	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12661378	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12661702	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12662426	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12664091	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12664768	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13190751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13195545	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198459	0.82[JPT][hapmap]
rs13200310	0.83[ASN][1000 genomes]
rs13203867	0.82[JPT][hapmap]
rs13205214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13205311	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13206035	0.94[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13207526	0.82[JPT][hapmap]
rs13210967	0.82[JPT][hapmap]
rs13219500	0.82[JPT][hapmap]
rs16890185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16890194	0.82[JPT][hapmap]
rs16890267	0.82[EUR][1000 genomes]
rs2025431	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2103950	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273441	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2274091	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2453882	0.82[JPT][hapmap]
rs2645096	0.82[JPT][hapmap]
rs2645098	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2645111	0.81[EUR][1000 genomes]
rs2645125	0.80[AMR][1000 genomes]
rs2645126	0.82[JPT][hapmap]
rs2645130	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2842499	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2842510	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2842511	0.93[YRI][hapmap]
rs2842514	0.82[JPT][hapmap]
rs2842516	0.82[JPT][hapmap]
rs2842521	0.94[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs2842524	0.82[JPT][hapmap]
rs34254045	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34450348	0.81[EUR][1000 genomes]
rs35122358	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35216205	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35772972	0.81[EUR][1000 genomes]
rs35849984	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3844314	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4394213	0.82[JPT][hapmap]
rs55679841	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55996712	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56023538	0.81[EUR][1000 genomes]
rs56129320	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56177150	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57402213	0.83[EUR][1000 genomes]
rs58333612	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58611435	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61411293	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6458032	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458037	0.82[JPT][hapmap]
rs6903743	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6906289	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6908106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6908761	0.82[JPT][hapmap]
rs6910180	0.85[JPT][hapmap]
rs6910837	0.82[JPT][hapmap]
rs6911481	1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs6911716	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6916535	0.82[JPT][hapmap]
rs6919884	0.82[JPT][hapmap]
rs6923132	0.82[JPT][hapmap]
rs6923254	0.82[JPT][hapmap]
rs6936260	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71569394	0.96[ASN][1000 genomes]
rs73419440	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7742226	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7745796	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7746266	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7747996	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7748312	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7750445	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7759145	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7759792	0.89[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7761561	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7762052	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7764130	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7773419	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7775794	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7776025	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6910715	STK38	cis	cerebellum	SCAN
rs6910715	KCTD20	cis	cerebellum	SCAN
rs6910715	FOXP4	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37767400-37777000	Weak transcription	Right Atrium	heart
2	chr6:37774600-37777400	Enhancers	Fetal Brain Male	brain
3	chr6:37775200-37777400	Enhancers	Fetal Kidney	kidney
4	chr6:37775200-37777400	Enhancers	Fetal Muscle Leg	muscle
5	chr6:37775200-37777400	Enhancers	HSMMtube	muscle
6	chr6:37775200-37777600	Enhancers	HMEC	breast
7	chr6:37775400-37777200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:37775400-37777400	Enhancers	Placenta	Placenta
9	chr6:37775400-37777400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:37775400-37777400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:37775400-37777600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:37775400-37777600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:37775800-37777000	Weak transcription	Esophagus	oesophagus
14	chr6:37775800-37777200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:37775800-37777200	Weak transcription	Psoas Muscle	Psoas
16	chr6:37775800-37777400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:37776000-37785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:37776200-37777400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:37776400-37777000	Weak transcription	HSMM	muscle
20	chr6:37776400-37777400	Enhancers	Brain Anterior Caudate	brain
21	chr6:37776400-37777400	Enhancers	Ovary	ovary
22	chr6:37776400-37785800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:37776600-37777000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:37776600-37777200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr6:37776600-37777400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:37776600-37777400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:37776600-37777400	Enhancers	Brain Hippocampus Middle	brain
28	chr6:37776800-37777000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:37776800-37777200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:37776800-37777200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:37776800-37777400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:37776800-37777400	Enhancers	Adipose Nuclei	Adipose
33	chr6:37776800-37777400	Enhancers	Liver	Liver
34	chr6:37776800-37777400	Enhancers	Brain Angular Gyrus	brain
35	chr6:37776800-37777400	Bivalent Enhancer	Fetal Stomach	stomach
36	chr6:37776800-37777400	Enhancers	NHDF-Ad	bronchial
37	chr6:37776800-37777400	Flanking Active TSS	NHEK	skin

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