Variant report

Variant	rs7780269
Chromosome Location	chr7:6316798-6316799
allele	C/T
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	CTCF	chr7:6316740-6316890	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6310402..6314489-chr7:6314854..6318602,7	K562	blood:
2	chr7:6311447..6314640-chr7:6315943..6318631,5	K562	blood:
3	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:59)

rs_ID	r²[population]
rs10046499	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10224504	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10225119	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10226743	0.83[CHD][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][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];0.83[CHD][hapmap]
rs10255662	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10255914	1.00[JPT][hapmap]
rs10261217	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]
rs10263878	0.88[ASN][1000 genomes]
rs10267982	1.00[JPT][hapmap]
rs10275021	1.00[CHB][hapmap];0.83[CHD][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12667392	1.00[JPT][hapmap]
rs13437890	1.00[JPT][hapmap]
rs17136048	0.83[CHD][hapmap];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[CHD][hapmap];1.00[GIH][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6942707	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6944071	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6946205	0.83[CHD][hapmap];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]
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];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958329	0.83[CHD][hapmap];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:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
rs7780269	STK10	trans	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6312600-6320000	Enhancers	Placenta	Placenta
2	chr7:6313000-6321600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:6313000-6322600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:6313000-6322800	Weak transcription	Osteobl	bone
5	chr7:6313200-6316800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:6313200-6322600	Weak transcription	Stomach Mucosa	stomach
7	chr7:6313400-6318800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:6313400-6322000	Weak transcription	Hela-S3	cervix
9	chr7:6313400-6322600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:6313400-6322600	Weak transcription	Ovary	ovary
11	chr7:6315800-6317000	Enhancers	NHEK	skin
12	chr7:6315800-6317200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr7:6315800-6317200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:6315800-6317400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:6315800-6317400	Enhancers	NHLF	lung
16	chr7:6315800-6317600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:6316000-6317000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:6316000-6317200	Enhancers	NHDF-Ad	bronchial
19	chr7:6316000-6317400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr7:6316200-6316800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:6316200-6317000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:6316200-6317200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:6316200-6317400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr7:6316200-6317400	Enhancers	A549	lung
25	chr7:6316400-6317000	Enhancers	Fetal Stomach	stomach
26	chr7:6316400-6317000	Enhancers	NH-A	brain
27	chr7:6316400-6317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:6316400-6317400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:6316400-6317400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:6316600-6317000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr7:6316600-6317200	Enhancers	HSMM	muscle
32	chr7:6316600-6317200	Weak transcription	HSMMtube	muscle
33	chr7:6316600-6317400	Enhancers	HMEC	breast
34	chr7:6316600-6317400	Enhancers	K562	blood
35	chr7:6316600-6322800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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