Variant report

Variant	rs9495636
Chromosome Location	chr6:140399553-140399554
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	RXRA	chr6:140399292-140400367	SK-N-SH	brain:	n/a	chr6:140399847-140399866 chr6:140399747-140399761
2	NFIC	chr6:140399390-140400508	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr6:140399170-140400506	SK-N-SH	brain:	n/a	chr6:140399809-140399819
4	JUND	chr6:140399500-140400428	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:140398883-140400316	SK-N-MC	brain:	n/a	n/a
6	EP300	chr6:140399163-140400467	SK-N-SH	brain:	n/a	n/a
7	EP300	chr6:140398916-140400498	SK-N-SH	brain:	n/a	chr6:140399131-140399140
8	TCF12	chr6:140398903-140401059	SK-N-SH	brain:	n/a	chr6:140399809-140399819 chr6:140399088-140399095
9	PBX3	chr6:140399045-140400372	SK-N-SH	brain:	n/a	chr6:140399362-140399371
10	TEAD4	chr6:140399220-140400379	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr6:140398904-140400878	SK-N-SH	brain:	n/a	chr6:140400561-140400577 chr6:140400563-140400575 chr6:140400565-140400574
12	JUND	chr6:140399311-140400379	SK-N-SH	brain:	n/a	chr6:140399464-140399476
13	GATA3	chr6:140399110-140400947	SK-N-SH	brain:	n/a	chr6:140400561-140400577 chr6:140400563-140400575 chr6:140400565-140400574
14	POLR2A	chr6:140399409-140400743	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr6:140399534-140400453	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:140398877..140401042-chr6:140404023..140406450,2	K562	blood:
2	chr6:139696210..139697933-chr6:140398822..140400886,2	K562	blood:
3	chr6:140390060..140392664-chr6:140397671..140399616,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236013	TF binding region
ENSG00000236013	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13204837	0.88[YRI][hapmap]
rs1416289	0.88[YRI][hapmap]
rs592056	0.88[YRI][hapmap]
rs618515	0.90[YRI][hapmap]
rs647968	0.90[YRI][hapmap]
rs6931550	1.00[AMR][1000 genomes]
rs6931710	1.00[AMR][1000 genomes]
rs724061	0.90[YRI][hapmap]
rs7774706	0.82[YRI][hapmap]
rs9399298	0.90[YRI][hapmap]
rs9403134	0.90[YRI][hapmap]
rs9495641	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9495648	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140393000-140400000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:140393000-140400400	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:140393000-140400600	Weak transcription	Ovary	ovary
4	chr6:140393600-140400400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:140394000-140400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:140394400-140403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:140395000-140400000	Weak transcription	Hela-S3	cervix
8	chr6:140396600-140399600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:140398400-140399600	Enhancers	NHLF	lung
10	chr6:140398400-140400800	Enhancers	HSMM	muscle
11	chr6:140398400-140401800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:140398600-140400600	Weak transcription	Left Ventricle	heart
13	chr6:140398800-140400200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:140398800-140400400	Enhancers	Osteobl	bone
15	chr6:140398800-140400800	Enhancers	HUVEC	blood vessel
16	chr6:140398800-140401000	Enhancers	Colon Smooth Muscle	Colon
17	chr6:140398800-140401800	Enhancers	Fetal Heart	heart
18	chr6:140399000-140400400	Enhancers	HSMMtube	muscle
19	chr6:140399000-140400600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:140399000-140400800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:140399000-140401000	Enhancers	NH-A	brain
22	chr6:140399000-140401800	Enhancers	Fetal Lung	lung
23	chr6:140399200-140399600	Enhancers	Fetal Kidney	kidney
24	chr6:140399200-140399600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:140399200-140399800	Flanking Active TSS	NHDF-Ad	bronchial
26	chr6:140399200-140400600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:140399200-140400800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:140399200-140401000	Enhancers	Adipose Nuclei	Adipose
29	chr6:140399400-140399600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:140399400-140399800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:140399400-140399800	Weak transcription	Fetal Stomach	stomach
32	chr6:140399400-140400200	Enhancers	Fetal Brain Male	brain
33	chr6:140399400-140400400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:140399400-140400400	Enhancers	Brain Angular Gyrus	brain
35	chr6:140399400-140400800	Enhancers	Rectal Smooth Muscle	rectum
36	chr6:140399400-140404000	Weak transcription	Fetal Intestine Small	intestine

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