Variant report

Variant	rs3778021
Chromosome Location	chr6:36948805-36948806
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	CTCF	chr6:36948800-36948950	HEEpiC	esophagus:	n/a	chr6:36948861-36948879
2	CTCF	chr6:36948780-36948930	AG09319	gingival:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
3	CTCF	chr6:36948773-36948924	MCF-7	breast:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
4	POLR2A	chr6:36948707-36948910	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:36948780-36948930	GM12873	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
6	CTCF	chr6:36948784-36948944	GM12892	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
7	CTCF	chr6:36948780-36948930	HCFaa	heart:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
8	CTCF	chr6:36948740-36948890	HRPEpiC	eye:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
9	CTCF	chr6:36948760-36948910	HRPEpiC	eye:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
10	CTCF	chr6:36948800-36948950	BE2_C	brain:	n/a	chr6:36948861-36948879
11	CTCF	chr6:36948780-36948930	GM12878	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
12	CTCF	chr6:36948771-36948939	MCF-7	breast:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
13	CTCF	chr6:36948700-36949030	GM12878	blood:	n/a	chr6:36948861-36948879 chr6:36948973-36948986 chr6:36948787-36948795
14	CTCF	chr6:36948760-36948910	AG04449	skin:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
15	CTCF	chr6:36948800-36948950	HCPEpiC	choroid plexus:	n/a	chr6:36948861-36948879
16	CTCF	chr6:36948760-36948910	GM06990	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
17	CTCF	chr6:36948740-36948890	RPTEC	kidney:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
18	POLR2A	chr6:36948399-36948935	K562	blood:	n/a	n/a
19	CTCF	chr6:36948780-36948930	HPAF	blood vessel:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
20	TEAD4	chr6:36948681-36949096	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:36948492-36949305	K562	blood:	n/a	n/a
22	CTCF	chr6:36948780-36948930	AG10803	skin:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
23	CTCF	chr6:36948767-36949045	IMR90	lung:	n/a	chr6:36948861-36948879 chr6:36948973-36948986 chr6:36948787-36948795
24	CTCF	chr6:36948753-36948911	MCF-7	breast:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
25	CTCF	chr6:36948780-36948930	HBMEC	blood vessel:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
26	CTCF	chr6:36948756-36948935	H1-hESC	embryonic stem cell:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
27	POLR2A	chr6:36946683-36950240	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:36948633-36948912	HepG2	liver:	n/a	n/a
29	CTCF	chr6:36948760-36948910	Hela-S3	cervix:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
30	CTCF	chr6:36948779-36948937	Hela-S3	cervix:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
31	POLR2A	chr6:36948684-36950367	GM12878	blood:	n/a	n/a
32	CTCF	chr6:36948804-36948908	GM12891	blood:	n/a	chr6:36948861-36948879
33	CTCF	chr6:36948720-36948870	NHDF-neo	bronchial:	n/a	chr6:36948787-36948795
34	RAD21	chr6:36948717-36949086	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr6:36948796-36948919	GM19238	blood:	n/a	chr6:36948861-36948879
36	CTCF	chr6:36948720-36948870	GM12869	blood:	n/a	chr6:36948787-36948795
37	CTCF	chr6:36948793-36948908	ProgFib	skin:	n/a	chr6:36948861-36948879
38	CTCF	chr6:36948740-36948890	SAEC	small airway:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
39	CTCF	chr6:36948720-36948870	HFF-Myc	foreskin:	n/a	chr6:36948787-36948795
40	CTCF	chr6:36948740-36948890	WERI-Rb-1	eye:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
41	TCF12	chr6:36948766-36949028	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:36948623-36949742	GM12892	blood:	n/a	n/a
43	CTCF	chr6:36948800-36948950	GM12874	blood:	n/a	chr6:36948861-36948879
44	POLR2A	chr6:36948480-36949698	K562	blood:	n/a	n/a
45	CTCF	chr6:36948720-36948870	MCF-7	breast:	n/a	chr6:36948787-36948795
46	ZNF143	chr6:36948746-36949028	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr6:36948769-36948937	GM19239	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
48	CTCF	chr6:36948800-36948950	HRE	kidney:	n/a	chr6:36948861-36948879
49	CTCF	chr6:36948740-36948890	GM12867	blood:	n/a	chr6:36948861-36948879 chr6:36948787-36948795
50	CTCF	chr6:36948700-36948850	GM12872	blood:	n/a	chr6:36948787-36948795

No.	Distal block	Cell Line	Cell type
1	chr6:36937337..36939324-chr6:36946513..36949209,3	MCF-7	breast:
2	chr6:36937337..36939387-chr6:36947202..36951298,3	MCF-7	breast:
3	chr6:36947258..36950041-chr6:36986048..36987573,2	MCF-7	breast:
4	chr6:36853647..36856578-chr6:36948651..36952350,3	K562	blood:
5	chr6:36948207..36949609-chr6:36985741..36986646,4	MCF-7	breast:

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs831506	0.82[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription 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	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3778021	PI16	cis	parietal	SCAN
rs3778021	TSPO2	cis	cerebellum	SCAN
rs3778021	ZFAND3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:36934200-36949200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:36934400-36949200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:36934600-36949200	Strong transcription	Placenta	Placenta
8	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:36935000-36949800	Genic enhancers	Left Ventricle	heart
10	chr6:36935000-36950200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:36936200-36949000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr6:36939000-36951200	Strong transcription	HSMM	muscle
13	chr6:36939400-36949600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:36939600-36950600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:36941200-36950600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:36944000-36949400	Genic enhancers	Right Ventricle	heart
17	chr6:36945000-36949200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:36945000-36951200	Enhancers	Fetal Heart	heart
19	chr6:36945400-36951400	Weak transcription	Fetal Kidney	kidney
20	chr6:36945600-36949400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:36945600-36949800	Genic enhancers	Stomach Smooth Muscle	stomach
22	chr6:36946200-36949000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:36946200-36951000	Weak transcription	Small Intestine	intestine
24	chr6:36946200-36952000	Weak transcription	A549	lung
25	chr6:36946400-36949400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:36946400-36949600	Genic enhancers	Fetal Muscle Leg	muscle
27	chr6:36946400-36949800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:36946400-36950400	Weak transcription	Ovary	ovary
29	chr6:36946400-36951200	Weak transcription	Hela-S3	cervix
30	chr6:36946400-36951600	Weak transcription	HSMMtube	muscle
31	chr6:36946400-36951800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:36946600-36949200	Weak transcription	Colonic Mucosa	Colon
33	chr6:36946600-36949200	Enhancers	Fetal Lung	lung
34	chr6:36946600-36949600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:36946600-36950600	Weak transcription	HUVEC	blood vessel
36	chr6:36946600-36950600	Weak transcription	NHDF-Ad	bronchial
37	chr6:36946600-36951200	Weak transcription	HMEC	breast
38	chr6:36946800-36949200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:36946800-36949200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:36946800-36949400	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr6:36946800-36949800	Enhancers	Brain Hippocampus Middle	brain
42	chr6:36946800-36949800	Genic enhancers	Fetal Thymus	thymus
43	chr6:36946800-36949800	Enhancers	Pancreas	Pancrea
44	chr6:36946800-36949800	Enhancers	Right Atrium	heart
45	chr6:36946800-36950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:36946800-36950800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:36946800-36951000	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr6:36946800-36951800	Enhancers	Brain Angular Gyrus	brain
49	chr6:36946800-36951800	Genic enhancers	Brain Anterior Caudate	brain
50	chr6:36947000-36949200	Genic enhancers	Liver	Liver

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