Variant report

Variant	rs10261217
Chromosome Location	chr7:6314679-6314680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:6313860-6314848	SK-N-SH	brain:	n/a	chr7:6314021-6314042 chr7:6314028-6314035 chr7:6314026-6314035 chr7:6314028-6314035 chr7:6314028-6314035 chr7:6314026-6314036
2	REST	chr7:6314550-6314875	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:6310562..6312865-chr7:6314382..6316980,2	MCF-7	breast:

Variant related genes	Relation type
CYTH3	TF binding region
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10046499	1.00[JPT][hapmap]
rs10224504	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10225119	1.00[JPT][hapmap]
rs10227013	1.00[ASN][1000 genomes]
rs10229323	0.87[ASN][1000 genomes]
rs10235115	0.93[ASN][1000 genomes]
rs10240510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10241174	1.00[JPT][hapmap]
rs10241580	0.83[ASN][1000 genomes]
rs10244640	1.00[JPT][hapmap]
rs10245186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10247585	1.00[JPT][hapmap]
rs10252947	1.00[JPT][hapmap]
rs10253501	1.00[JPT][hapmap]
rs10255598	1.00[CHB][hapmap]
rs10255662	1.00[JPT][hapmap]
rs10255914	1.00[JPT][hapmap]
rs10263878	0.88[ASN][1000 genomes]
rs10267982	1.00[JPT][hapmap]
rs10275021	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10279137	1.00[JPT][hapmap]
rs10280585	1.00[JPT][hapmap]
rs11760468	0.93[ASN][1000 genomes]
rs11768047	1.00[JPT][hapmap]
rs11768749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12667392	1.00[JPT][hapmap]
rs13437890	1.00[JPT][hapmap]
rs17136048	1.00[JPT][hapmap]
rs34623646	0.93[ASN][1000 genomes]
rs58052451	0.93[ASN][1000 genomes]
rs59100979	0.93[ASN][1000 genomes]
rs59568570	1.00[ASN][1000 genomes]
rs6463540	1.00[JPT][hapmap]
rs6463541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6463542	1.00[ASN][1000 genomes]
rs6463543	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6463544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6942707	1.00[JPT][hapmap]
rs6944071	1.00[JPT][hapmap]
rs6946205	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6949823	1.00[JPT][hapmap]
rs6955065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6960965	1.00[JPT][hapmap]
rs6961095	0.88[ASN][1000 genomes]
rs6962767	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6969814	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6969863	1.00[JPT][hapmap]
rs6976305	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7777433	1.00[JPT][hapmap]
rs7780269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783018	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7784025	0.83[ASN][1000 genomes]
rs7791225	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7800777	1.00[JPT][hapmap]
rs7807841	1.00[JPT][hapmap]
rs7811702	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958329	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9986688	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
16	nsv538715	chr7:6308902-6359025	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv1020251	chr7:6309528-6379941	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10261217	STK10	trans	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6312600-6320000	Enhancers	Placenta	Placenta
2	chr7:6312800-6316000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:6312800-6316400	Weak transcription	HSMMtube	muscle
4	chr7:6312800-6316400	Weak transcription	NH-A	brain
5	chr7:6313000-6315400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:6313000-6315800	Weak transcription	NHEK	skin
7	chr7:6313000-6316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:6313000-6316400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:6313000-6316400	Weak transcription	Fetal Stomach	stomach
10	chr7:6313000-6316600	Weak transcription	HMEC	breast
11	chr7:6313000-6316600	Weak transcription	HSMM	muscle
12	chr7:6313000-6321600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:6313000-6322600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:6313000-6322800	Weak transcription	Osteobl	bone
15	chr7:6313200-6315800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:6313200-6315800	Weak transcription	NHLF	lung
17	chr7:6313200-6316000	Weak transcription	NHDF-Ad	bronchial
18	chr7:6313200-6316400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:6313200-6316800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:6313200-6322600	Weak transcription	Stomach Mucosa	stomach
21	chr7:6313400-6315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:6313400-6318800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:6313400-6322000	Weak transcription	Hela-S3	cervix
24	chr7:6313400-6322600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:6313400-6322600	Weak transcription	Ovary	ovary
26	chr7:6313600-6315800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:6314000-6316000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:6314000-6316200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:6314000-6316200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:6314200-6316600	Weak transcription	K562	blood
31	chr7:6314400-6316200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:6314400-6316200	Weak transcription	A549	lung

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