Variant report

Variant	rs10261757
Chromosome Location	chr7:139473243-139473244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr7:139472803-139473269	HepG2	liver:	n/a	n/a
2	RUNX3	chr7:139473136-139474016	GM12878	blood:	n/a	n/a
3	RUNX3	chr7:139472693-139473587	GM12878	blood:	n/a	n/a
4	JUND	chr7:139472599-139474783	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:139472005..139473850-chr7:139702644..139704624,2	K562	blood:
2	chr7:139466166..139468375-chr7:139473040..139475518,2	MCF-7	breast:
3	chr7:139468774..139474214-chr7:139474318..139478750,13	MCF-7	breast:
4	chr7:139472264..139474363-chr7:139641675..139643292,2	K562	blood:

No data

Variant related genes	Relation type
TBXAS1	TF binding region
ENSG00000059377	Chromatin interaction
ENSG00000064393	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10228448	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10228830	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10252208	1.00[MEX][hapmap]
rs10255449	1.00[MEX][hapmap]
rs10257315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10257659	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261500	1.00[MEX][hapmap]
rs10261622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10271046	1.00[MEX][hapmap]
rs10274540	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10278165	0.84[AMR][1000 genomes]
rs17161128	1.00[MEX][hapmap]
rs17161198	1.00[MEX][hapmap]
rs17161200	1.00[MEX][hapmap]
rs17161201	1.00[MEX][hapmap]
rs17161202	1.00[MEX][hapmap]
rs17161230	1.00[MEX][hapmap]
rs17161272	1.00[MEX][hapmap]
rs1859568	1.00[MEX][hapmap]
rs2158667	1.00[MEX][hapmap]
rs4529	1.00[MEX][hapmap]
rs60526073	0.90[AFR][1000 genomes]
rs6947799	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6954520	1.00[MEX][hapmap]
rs6963499	1.00[MEX][hapmap]
rs6963553	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6964028	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6972460	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73735621	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7455629	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs7777901	1.00[MEX][hapmap]
rs7810177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139440600-139474600	Weak transcription	Fetal Brain Male	brain
2	chr7:139446600-139475800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:139446600-139476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:139446800-139476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:139454200-139474000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:139455000-139475000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:139455200-139473400	Weak transcription	Fetal Brain Female	brain
8	chr7:139459600-139474400	Weak transcription	Fetal Intestine Large	intestine
9	chr7:139463600-139475000	Weak transcription	Ovary	ovary
10	chr7:139465600-139475000	Enhancers	Brain Substantia Nigra	brain
11	chr7:139467600-139475400	Weak transcription	Aorta	Aorta
12	chr7:139467800-139475000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:139468000-139475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:139468200-139474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:139468600-139473400	Weak transcription	Fetal Lung	lung
16	chr7:139468600-139474200	Weak transcription	K562	blood
17	chr7:139468800-139474200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:139468800-139474800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr7:139468800-139475000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:139468800-139475000	Weak transcription	Placenta	Placenta
21	chr7:139468800-139475600	Enhancers	Primary T cells from cord blood	blood
22	chr7:139469000-139475000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:139469000-139475400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:139469000-139475600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr7:139469200-139473400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr7:139469200-139473800	Weak transcription	Fetal Kidney	kidney
27	chr7:139469200-139474800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:139469200-139474800	Weak transcription	Colonic Mucosa	Colon
29	chr7:139469200-139474800	Weak transcription	Fetal Muscle Leg	muscle
30	chr7:139469200-139475400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:139469200-139475800	Weak transcription	Esophagus	oesophagus
32	chr7:139469200-139476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:139469200-139476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:139469600-139474800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:139469600-139475200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr7:139469800-139475800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:139470000-139473400	Weak transcription	Right Ventricle	heart
38	chr7:139470000-139475000	Weak transcription	Fetal Stomach	stomach
39	chr7:139470200-139475200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr7:139470400-139474400	Enhancers	Brain Hippocampus Middle	brain
41	chr7:139470400-139475000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:139470400-139475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:139470600-139475600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:139470800-139473600	Genic enhancers	HSMM	muscle
45	chr7:139471000-139473800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr7:139471000-139474600	Enhancers	Adipose Nuclei	Adipose
47	chr7:139471000-139474600	Genic enhancers	HepG2	liver
48	chr7:139471200-139473400	Weak transcription	Fetal Heart	heart
49	chr7:139471200-139473800	Enhancers	Pancreas	Pancrea
50	chr7:139471400-139475800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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