Variant report

Variant	rs2698716
Chromosome Location	chr7:26405353-26405354
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	RAD21	chr7:26403700-26406016	SK-N-SH	brain:	n/a	chr7:26404919-26404928 chr7:26404917-26404931 chr7:26404913-26404932
2	CTCF	chr7:26405220-26405370	HVMF	connective:	n/a	n/a
3	CTCF	chr7:26404408-26405690	SK-N-SH	brain:	n/a	chr7:26404916-26404932 chr7:26404915-26404933 chr7:26404910-26404931 chr7:26404917-26404930
4	GATA1	chr7:26404800-26405957	PBDE	blood:	n/a	chr7:26405700-26405716 chr7:26405705-26405712 chr7:26405698-26405719 chr7:26405705-26405715
5	SMC3	chr7:26404541-26405871	SK-N-SH	brain:	n/a	chr7:26404917-26404931
6	CTCF	chr7:26405320-26405470	GM12871	blood:	n/a	n/a
7	CTCF	chr7:26405220-26405370	HAc	cerebellar:	n/a	n/a
8	CTCF	chr7:26404709-26405369	IMR90	lung:	n/a	chr7:26404916-26404932 chr7:26404915-26404933 chr7:26404910-26404931 chr7:26404917-26404930
9	ZNF143	chr7:26404767-26405448	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr7:26405300-26405450	GM12873	blood:	n/a	n/a
11	CTCF	chr7:26404185-26405437	A549	lung:	n/a	chr7:26404916-26404932 chr7:26404915-26404933 chr7:26404910-26404931 chr7:26404917-26404930

No.	Distal block	Cell Line	Cell type
1	chr7:25605629..25606130-chr7:26404535..26405453,2	K562	blood:
2	chr7:26238752..26241126-chr7:26401530..26405700,5	MCF-7	breast:
3	chr7:25932095..25933159-chr7:26404361..26405639,15	K562	blood:
4	chr7:26224710..26231544-chr7:26402048..26407320,8	K562	blood:
5	chr7:26238011..26242916-chr7:26400117..26407916,12	MCF-7	breast:
6	chr7:26330494..26332726-chr7:26403941..26406420,2	MCF-7	breast:
7	chr7:26223580..26226210-chr7:26405068..26407320,2	K562	blood:
8	chr7:26318268..26319062-chr7:26404447..26405880,6	MCF-7	breast:

Variant related genes	Relation type
SNX10	TF binding region
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000086300	Chromatin interaction
ENSG00000050344	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1320884	0.80[EUR][1000 genomes]
rs2253569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2698715	0.81[ASN][1000 genomes]
rs2698717	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2698718	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2699808	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2699809	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2699810	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2699811	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2698716	SNX10	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26375000-26414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:26384800-26409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:26385600-26414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:26387400-26409400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:26387800-26409400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:26388000-26409400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:26389000-26413200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:26397000-26409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:26398600-26415400	Weak transcription	HMEC	breast
10	chr7:26402600-26406200	Weak transcription	Lung	lung
11	chr7:26402600-26415200	Enhancers	Liver	Liver
12	chr7:26403200-26407600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:26403800-26415600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:26404000-26405400	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr7:26404200-26405800	Genic enhancers	GM12878-XiMat	blood
16	chr7:26404600-26405400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:26404600-26405400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr7:26404600-26405400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr7:26404600-26405400	Flanking Active TSS	Fetal Kidney	kidney
20	chr7:26404600-26405600	Genic enhancers	Fetal Intestine Small	intestine
21	chr7:26404600-26406200	Enhancers	Fetal Intestine Large	intestine
22	chr7:26404600-26407400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:26404600-26407400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:26404800-26406200	Weak transcription	Adipose Nuclei	Adipose
25	chr7:26404800-26406400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:26404800-26407000	Strong transcription	Dnd41	blood
27	chr7:26404800-26407600	Enhancers	Pancreas	Pancrea
28	chr7:26404800-26409400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:26404800-26409400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:26404800-26409600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:26404800-26411200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:26404800-26414000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:26404800-26415200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:26405000-26405800	Enhancers	K562	blood
35	chr7:26405000-26406200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr7:26405000-26407200	Strong transcription	Primary T cells from cord blood	blood
37	chr7:26405000-26407400	Strong transcription	Placenta	Placenta
38	chr7:26405000-26407400	Strong transcription	Spleen	Spleen
39	chr7:26405000-26407400	Strong transcription	HepG2	liver
40	chr7:26405000-26407600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr7:26405000-26407600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:26405000-26409000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:26405000-26409400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:26405000-26409400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr7:26405200-26405600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:26405200-26405600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:26405200-26405800	Enhancers	HUVEC	blood vessel
48	chr7:26405200-26406000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:26405200-26406400	Enhancers	Fetal Lung	lung
50	chr7:26405200-26406400	Enhancers	Fetal Stomach	stomach

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