Variant report

Variant	rs378373
Chromosome Location	chr6:166928580-166928581
allele	A/C
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	RAD21	chr6:166928492-166928895	SK-N-SH_RA	brain:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
2	JUN	chr6:166928489-166929142	K562	blood:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928791-166928804 chr6:166928762-166928770
3	RAD21	chr6:166928370-166929127	HCT-116	colon:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
4	FOS	chr6:166928576-166928994	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928760-166928771 chr6:166928762-166928770
5	FOSL1	chr6:166928365-166929187	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
6	FOSL1	chr6:166928422-166929142	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
7	CTCF	chr6:166928518-166928837	MCF-7	breast:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
8	POLR2A	chr6:166928568-166929065	U87	brain:	n/a	n/a
9	SMC3	chr6:166927598-166929040	SK-N-SH	brain:	n/a	chr6:166927823-166927837 chr6:166927823-166927830
10	RAD21	chr6:166928508-166928872	MCF-7	breast:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
11	FOS	chr6:166928575-166928969	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928760-166928771 chr6:166928762-166928770
12	CTCF	chr6:166928580-166928730	HFF-Myc	foreskin:	n/a	n/a
13	FOSL2	chr6:166928567-166928876	HepG2	liver:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
14	RCOR1	chr6:166927751-166929314	IMR90	lung:	n/a	n/a
15	TCF12	chr6:166928402-166929170	SK-N-SH	brain:	n/a	n/a
16	MAX	chr6:166928577-166928955	NB4	blood:	n/a	chr6:166928762-166928771 chr6:166928761-166928770
17	FOS	chr6:166928575-166929134	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
18	FOSL1	chr6:166928551-166928888	K562	blood:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928760-166928771 chr6:166928762-166928770
19	FOS	chr6:166928576-166929183	MCF10A-Er-Src	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
20	CTCF	chr6:166928580-166928730	BE2_C	brain:	n/a	n/a
21	PBX3	chr6:166928527-166929047	SK-N-SH	brain:	n/a	n/a
22	MAZ	chr6:166928202-166929095	IMR90	lung:	n/a	chr6:166928762-166928771 chr6:166928761-166928770
23	FOSL2	chr6:166928527-166928933	A549	lung:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
24	PBX3	chr6:166928528-166929160	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr6:166928491-166929023	SK-N-SH	brain:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
26	JUND	chr6:166928453-166929120	SK-N-SH	brain:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
27	FOS	chr6:166928495-166929204	HUVEC	blood vessel:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928760-166928771 chr6:166928762-166928770
28	JUND	chr6:166928462-166929134	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
29	FOSL2	chr6:166928486-166928945	MCF-7	breast:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166928762-166928770
30	TCF12	chr6:166928403-166929186	SK-N-SH	brain:	n/a	n/a
31	JUND	chr6:166928414-166929175	SK-N-SH	brain:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
32	JUND	chr6:166928485-166929139	SK-N-SH	brain:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
33	CTCF	chr6:166928527-166928927	IMR90	lung:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
34	RAD21	chr6:166928368-166929095	HCT-116	colon:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
35	CTCF	chr6:166928500-166928650	BE2_C	brain:	n/a	n/a
36	CTCF	chr6:166928500-166928650	HAc	cerebellar:	n/a	n/a
37	CTCF	chr6:166928405-166929033	HCT-116	colon:	n/a	chr6:166928822-166928835 chr6:166928742-166928755 chr6:166928722-166928731 chr6:166928746-166928755
38	JUND	chr6:166928409-166929160	HCT-116	colon:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
39	RAD21	chr6:166928549-166928881	SK-N-SH_RA	brain:	n/a	chr6:166928721-166928730 chr6:166928741-166928754 chr6:166928822-166928836
40	EP300	chr6:166928442-166929164	SK-N-SH	brain:	n/a	chr6:166928762-166928771 chr6:166928500-166928516
41	FOSL2	chr6:166928442-166929109	SK-N-SH	brain:	n/a	chr6:166928646-166928660 chr6:166928762-166928769 chr6:166929058-166929067 chr6:166928762-166928770
42	RAD21	chr6:166928497-166929042	IMR90	lung:	n/a	chr6:166928721-166928730 chr6:166928822-166928836 chr6:166928741-166928754

No.	Distal block	Cell Line	Cell type
1	chr6:166928469..166930058-chr6:167040238..167042581,2	MCF-7	breast:
2	chr6:166869518..166870276-chr6:166927954..166928779,2	MCF-7	breast:
3	chr6:166928192..166929030-chr6:167027760..167028686,4	MCF-7	breast:

Variant related genes	Relation type
RPS6KA2	TF binding region
ENSG00000071242	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1041918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187909	0.85[CHB][hapmap]
rs3799655	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	esv1806956	chr6:166928580-166938431	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs378373	THBS2	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166899400-166929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:166901000-166954800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:166902200-166954400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:166902600-166952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:166909600-166943800	Weak transcription	Colonic Mucosa	Colon
6	chr6:166912200-166931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:166913000-166929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:166913000-166952000	Weak transcription	Primary T cells from cord blood	blood
9	chr6:166916200-166954200	Weak transcription	Right Atrium	heart
10	chr6:166916400-166940400	Weak transcription	Fetal Heart	heart
11	chr6:166917200-166932000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:166918000-166928600	Weak transcription	HUVEC	blood vessel
13	chr6:166918200-166928600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:166918400-166931400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:166919200-166928600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:166921200-166930000	Weak transcription	Fetal Intestine Large	intestine
17	chr6:166921400-166930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:166921400-166930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:166921400-166943600	Weak transcription	Fetal Lung	lung
20	chr6:166921600-166932000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:166921600-166932000	Weak transcription	Fetal Kidney	kidney
22	chr6:166921600-166937400	Weak transcription	Fetal Brain Male	brain
23	chr6:166922400-166928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:166922400-166929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:166923000-166930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:166923000-166930000	Weak transcription	Esophagus	oesophagus
27	chr6:166923000-166931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:166923000-166937200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:166923000-166940400	Weak transcription	Aorta	Aorta
30	chr6:166923000-166943800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:166923200-166931200	Weak transcription	Brain Germinal Matrix	brain
32	chr6:166923200-166932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:166923200-166940200	Weak transcription	Ovary	ovary
34	chr6:166923200-166943200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:166923200-166943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:166923600-166928600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:166923600-166936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:166923800-166930000	Weak transcription	Placenta	Placenta
39	chr6:166923800-166944400	Weak transcription	Psoas Muscle	Psoas
40	chr6:166923800-166953000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:166924600-166928800	Weak transcription	HSMMtube	muscle
42	chr6:166925000-166940400	Weak transcription	Adipose Nuclei	Adipose
43	chr6:166926200-166928600	Weak transcription	Osteobl	bone
44	chr6:166926200-166929000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr6:166926200-166930400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:166926200-166930400	Strong transcription	Fetal Stomach	stomach
47	chr6:166926400-166929200	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:166926600-166928800	Strong transcription	Pancreas	Pancrea
49	chr6:166926600-166928800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:166927000-166929000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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