Variant report

Variant	rs2179996
Chromosome Location	chr6:140175382-140175383
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	RFX5	chr6:140174512-140175504	IMR90	lung:	n/a	n/a
2	GATA3	chr6:140175361-140175957	T-47D	breast:	n/a	n/a
3	EP300	chr6:140175287-140176181	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139694169..139695837-chr6:140173549..140176425,2	K562	blood:

Variant related genes	Relation type
ENSG00000231426	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11963806	1.00[ASN][1000 genomes]
rs12110570	1.00[ASN][1000 genomes]
rs17811355	0.81[AMR][1000 genomes]
rs2144165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179995	1.00[ASN][1000 genomes]
rs2207334	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001016	1.00[ASN][1000 genomes]
rs3015438	1.00[ASN][1000 genomes]
rs3918473	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3946063	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403279	1.00[ASN][1000 genomes]
rs4554334	0.81[AMR][1000 genomes]
rs4896490	0.81[AMR][1000 genomes]
rs4896491	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs4896492	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55772636	0.81[AMR][1000 genomes]
rs6570382	1.00[ASN][1000 genomes]
rs6570383	1.00[ASN][1000 genomes]
rs6900161	1.00[ASN][1000 genomes]
rs6900843	1.00[ASN][1000 genomes]
rs6912157	1.00[ASN][1000 genomes]
rs6917570	1.00[ASN][1000 genomes]
rs6917808	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939887	1.00[ASN][1000 genomes]
rs72986790	1.00[ASN][1000 genomes]
rs73778053	0.81[AMR][1000 genomes]
rs73778057	0.81[AMR][1000 genomes]
rs73778058	0.81[AMR][1000 genomes]
rs7743495	1.00[ASN][1000 genomes]
rs7745714	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746560	1.00[ASN][1000 genomes]
rs7750105	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761684	1.00[ASN][1000 genomes]
rs7762012	1.00[ASN][1000 genomes]
rs7768688	1.00[ASN][1000 genomes]
rs7775904	1.00[ASN][1000 genomes]
rs9376470	1.00[ASN][1000 genomes]
rs9399296	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140168800-140177000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:140169000-140177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:140172200-140178800	Enhancers	Fetal Intestine Small	intestine
4	chr6:140172200-140179000	Enhancers	Fetal Intestine Large	intestine
5	chr6:140173000-140175400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:140173200-140175400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:140173200-140177000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:140173400-140175400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:140173400-140178600	Enhancers	Colon Smooth Muscle	Colon
10	chr6:140173400-140178600	Enhancers	Osteobl	bone
11	chr6:140173400-140180200	Enhancers	Fetal Kidney	kidney
12	chr6:140173400-140182200	Enhancers	Rectal Smooth Muscle	rectum
13	chr6:140173600-140175800	Enhancers	NHDF-Ad	bronchial
14	chr6:140173800-140175400	Enhancers	Liver	Liver
15	chr6:140173800-140176000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:140174600-140175400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr6:140174600-140187000	Weak transcription	Psoas Muscle	Psoas
18	chr6:140174800-140176800	Weak transcription	NH-A	brain
19	chr6:140174800-140177000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:140174800-140177000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:140174800-140177000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:140174800-140177000	Weak transcription	Fetal Lung	lung
23	chr6:140174800-140177000	Weak transcription	Ovary	ovary
24	chr6:140174800-140177200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:140174800-140177200	Weak transcription	K562	blood
26	chr6:140175000-140175400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:140175000-140176400	Weak transcription	HSMM	muscle
28	chr6:140175000-140177000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:140175200-140175600	Weak transcription	NHLF	lung
30	chr6:140175200-140177000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:140175200-140177000	Weak transcription	Fetal Stomach	stomach
32	chr6:140175200-140179400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:140175200-140179800	Weak transcription	Rectal Mucosa Donor 31	rectum

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