Variant report

Variant	rs6953530
Chromosome Location	chr7:127586647-127586648
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	POLR2A	chr7:127586625-127586748	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:127586545-127586671	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127578537..127581052-chr7:127586207..127588657,2	K562	blood:

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1019578	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10228031	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1025075	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10487503	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1073155	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12536253	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1440973	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1468702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17133046	1.00[EUR][1000 genomes]
rs17151515	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17151567	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17151575	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17151629	1.00[EUR][1000 genomes]
rs17151639	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17151650	1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17151837	1.00[EUR][1000 genomes]
rs1833146	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1966517	1.00[EUR][1000 genomes]
rs2402873	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs325438	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325439	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325443	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325448	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325449	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325450	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757772	1.00[JPT][hapmap]
rs4728078	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4728082	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4731379	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4731382	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4731383	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4731384	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4731390	1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731391	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58395975	1.00[EUR][1000 genomes]
rs61743021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6467142	0.83[ASN][1000 genomes]
rs6467146	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6467147	0.83[ASN][1000 genomes]
rs6467149	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6467150	0.83[ASN][1000 genomes]
rs6467151	0.83[ASN][1000 genomes]
rs6467154	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6946590	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6950211	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6952123	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6964714	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6972398	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6972816	0.95[ASN][1000 genomes]
rs6975274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979918	0.83[ASN][1000 genomes]
rs698409	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs712720	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73721253	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73721258	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73721261	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73721264	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783560	1.00[EUR][1000 genomes]
rs7791000	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7794328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7804310	1.00[EUR][1000 genomes]
rs7809182	1.00[JPT][hapmap]

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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127562200-127589800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:127568200-127594000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:127569800-127615600	Weak transcription	Colonic Mucosa	Colon
4	chr7:127570000-127591400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:127570600-127615600	Weak transcription	Small Intestine	intestine
6	chr7:127570600-127615800	Weak transcription	Esophagus	oesophagus
7	chr7:127570600-127616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:127570800-127589200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:127570800-127599600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:127570800-127618200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:127571000-127615600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:127571000-127615800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:127571400-127589800	Weak transcription	Fetal Stomach	stomach
14	chr7:127571400-127617800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:127571600-127594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:127571600-127618000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:127571800-127602800	Weak transcription	Aorta	Aorta
18	chr7:127573200-127588600	Weak transcription	Ovary	ovary
19	chr7:127574400-127587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:127576400-127589000	Weak transcription	Fetal Kidney	kidney
21	chr7:127576400-127607000	Weak transcription	Spleen	Spleen
22	chr7:127576400-127615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:127577400-127588000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:127577800-127587400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:127577800-127588000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:127578000-127588400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:127578000-127588800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr7:127578000-127588800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:127578200-127616200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:127578800-127600200	Weak transcription	Stomach Mucosa	stomach
31	chr7:127579400-127592600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr7:127580400-127588000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:127581000-127588000	Strong transcription	Liver	Liver
34	chr7:127581000-127588600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:127581000-127594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:127581200-127587800	Weak transcription	Fetal Intestine Large	intestine
37	chr7:127581200-127615400	Weak transcription	Gastric	stomach
38	chr7:127582400-127589400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:127583200-127630600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:127583800-127595800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:127583800-127599000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:127584000-127589000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:127584000-127594000	Weak transcription	Adipose Nuclei	Adipose
44	chr7:127584000-127600000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:127584200-127589000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:127584200-127593400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:127584200-127600000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:127584200-127607000	Weak transcription	Right Ventricle	heart
49	chr7:127584400-127588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:127584400-127589000	Weak transcription	Dnd41	blood

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