Variant report

Variant	rs6964028
Chromosome Location	chr7:139474129-139474130
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	JUND	chr7:139473726-139474852	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr7:139473881-139474935	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr7:139474042-139474707	IMR90	lung:	n/a	n/a
4	SMC3	chr7:139473945-139477093	SK-N-SH	brain:	n/a	n/a
5	MEF2A	chr7:139473891-139474943	SK-N-SH	brain:	n/a	chr7:139473938-139473959
6	FOXM1	chr7:139473828-139474956	SK-N-SH	brain:	n/a	n/a
7	FOXM1	chr7:139474035-139474798	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr7:139473696-139475134	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr7:139473869-139474754	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr7:139474049-139474649	MCF10A-Er-Src	breast:	n/a	chr7:139474327-139474338
11	ZBTB33	chr7:139474043-139474640	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr7:139474079-139474658	MCF-7	breast:	n/a	n/a
13	TEAD4	chr7:139474045-139474838	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr7:139473783-139474933	SK-N-SH	brain:	n/a	n/a
15	EP300	chr7:139474081-139474550	Hela-S3	cervix:	n/a	chr7:139474302-139474309
16	POLR2A	chr7:139473925-139474925	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr7:139474121-139474550	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA3	chr7:139473607-139474975	SK-N-SH	brain:	n/a	chr7:139473659-139473668
19	FOS	chr7:139474129-139474517	MCF10A-Er-Src	breast:	n/a	chr7:139474327-139474338
20	MAX	chr7:139473899-139474707	SK-N-SH	brain:	n/a	n/a
21	MYC	chr7:139474031-139474449	MCF10A-Er-Src	breast:	n/a	n/a
22	FOSL2	chr7:139474033-139474589	A549	lung:	n/a	n/a
23	POLR2A	chr7:139473895-139475291	U87	brain:	n/a	n/a
24	NFIC	chr7:139474050-139474699	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr7:139473985-139474686	SK-N-SH	brain:	n/a	n/a
26	TCF12	chr7:139473679-139475005	SK-N-SH	brain:	n/a	n/a
27	MXI1	chr7:139473683-139479282	IMR90	lung:	n/a	n/a
28	JUND	chr7:139473791-139474880	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr7:139473858-139475002	U87	brain:	n/a	n/a
30	GATA3	chr7:139473996-139474792	A549	lung:	n/a	n/a
31	SIN3AK20	chr7:139473967-139474669	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr7:139473870-139477037	SK-N-SH	brain:	n/a	chr7:139475859-139475872 chr7:139474878-139474899 chr7:139475771-139475789 chr7:139475499-139475507
33	POLR2A	chr7:139473883-139475171	U87	brain:	n/a	n/a
34	EP300	chr7:139474095-139474727	SK-N-SH_RA	brain:	n/a	chr7:139474302-139474309
35	TEAD4	chr7:139473849-139474864	SK-N-SH	brain:	n/a	n/a
36	STAT3	chr7:139474053-139474539	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr7:139473812-139475008	U87	brain:	n/a	n/a
38	RXRA	chr7:139473821-139474910	SK-N-SH	brain:	n/a	n/a
39	MEF2A	chr7:139473849-139475064	SK-N-SH	brain:	n/a	chr7:139473938-139473959
40	TCF12	chr7:139473806-139474943	SK-N-SH	brain:	n/a	n/a
41	PBX3	chr7:139473858-139474988	SK-N-SH	brain:	n/a	n/a
42	EP300	chr7:139474115-139474730	SK-N-SH_RA	brain:	n/a	chr7:139474302-139474309
43	RXRA	chr7:139474067-139474869	SK-N-SH	brain:	n/a	n/a
44	FOSL2	chr7:139473813-139474825	SK-N-SH	brain:	n/a	n/a
45	JUND	chr7:139472599-139474783	SK-N-SH	brain:	n/a	n/a
46	ZBTB33	chr7:139474062-139474770	SK-N-SH	brain:	n/a	n/a
47	MAX	chr7:139473937-139474635	SK-N-SH	brain:	n/a	n/a
48	EP300	chr7:139473782-139474947	SK-N-SH	brain:	n/a	chr7:139474302-139474309
49	EP300	chr7:139473753-139474914	SK-N-SH	brain:	n/a	chr7:139474302-139474309
50	TAF1	chr7:139474050-139474588	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:139473245..139475405-chr7:139553701..139555890,2	K562	blood:
2	chr7:139466166..139468375-chr7:139473040..139475518,2	MCF-7	breast:
3	chr7:139328556..139330958-chr7:139473261..139475609,2	K562	blood:
4	chr7:139468774..139474214-chr7:139474318..139478750,13	MCF-7	breast:
5	chr7:139472264..139474363-chr7:139641675..139643292,2	K562	blood:
6	chr7:139465555..139467223-chr7:139473654..139475179,2	MCF-7	breast:

Variant related genes	Relation type
TBXAS1	TF binding region
ENSG00000064393	Chromatin interaction
ENSG00000059377	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	0.96[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	0.93[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]
rs10261757	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]
rs10271046	1.00[MEX][hapmap]
rs10274540	0.96[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];0.98[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6972460	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73735621	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7455629	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs7777901	1.00[MEX][hapmap]
rs7810177	0.96[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	chr7:139455000-139475000	Weak transcription	Fetal Intestine Small	intestine
6	chr7:139459600-139474400	Weak transcription	Fetal Intestine Large	intestine
7	chr7:139463600-139475000	Weak transcription	Ovary	ovary
8	chr7:139465600-139475000	Enhancers	Brain Substantia Nigra	brain
9	chr7:139467600-139475400	Weak transcription	Aorta	Aorta
10	chr7:139467800-139475000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr7:139468000-139475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:139468200-139474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:139468600-139474200	Weak transcription	K562	blood
14	chr7:139468800-139474200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:139468800-139474800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr7:139468800-139475000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:139468800-139475000	Weak transcription	Placenta	Placenta
18	chr7:139468800-139475600	Enhancers	Primary T cells from cord blood	blood
19	chr7:139469000-139475000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:139469000-139475400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:139469000-139475600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr7:139469200-139474800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:139469200-139474800	Weak transcription	Colonic Mucosa	Colon
24	chr7:139469200-139474800	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:139469200-139475400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr7:139469200-139475800	Weak transcription	Esophagus	oesophagus
27	chr7:139469200-139476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:139469200-139476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr7:139469600-139474800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:139469600-139475200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:139469800-139475800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:139470000-139475000	Weak transcription	Fetal Stomach	stomach
33	chr7:139470200-139475200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr7:139470400-139474400	Enhancers	Brain Hippocampus Middle	brain
35	chr7:139470400-139475000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:139470400-139475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:139470600-139475600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:139471000-139474600	Enhancers	Adipose Nuclei	Adipose
39	chr7:139471000-139474600	Genic enhancers	HepG2	liver
40	chr7:139471400-139475800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:139471600-139474200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:139471600-139475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:139471800-139474200	Enhancers	Gastric	stomach
44	chr7:139471800-139474800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:139471800-139475400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:139472000-139474200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:139472000-139475200	Enhancers	HMEC	breast
48	chr7:139472000-139475400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:139472000-139475400	Weak transcription	Small Intestine	intestine
50	chr7:139472000-139475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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