Variant report

Variant	rs6792759
Chromosome Location	chr3:150138424-150138425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150135087-150138468	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:150138414-150138464	T-47D	breast:	n/a
2	chr3:150138414-150138464	Hepatocyte	liver:	n/a
3	chr3:150138414-150138464	NH-A	brain:	n/a
4	chr3:150138414-150138464	HepG2	liver:	n/a
5	chr3:150138414-150138464	BE2_C	brain:	n/a
6	chr3:150138414-150138464	HEK293	kidney:	embryo
7	chr3:150138414-150138464	ECC-1	luminal epithelium:	n/a
8	chr3:150138414-150138464	NHDF-neo	bronchial:	n/a
9	chr3:150138414-150138464	RPTEC	kidney:	n/a
10	chr3:150138414-150138464	SKMC	muscle:	n/a
11	chr3:150138414-150138464	IMR90	lung:	fetal
12	chr3:150138414-150138464	HCM	heart:	n/a
13	chr3:150138414-150138464	PrEC	prostate:	n/a
14	chr3:150138414-150138464	Hela-S3	cervix:	n/a
15	chr3:150138414-150138464	AG09319	gingival:	n/a
16	chr3:150138414-150138464	Caco-2	colon:	n/a
17	chr3:150138414-150138464	ovcar-3	ovarian:	n/a
18	chr3:150138414-150138464	HUVEC	blood vessel:	n/a
19	chr3:150138414-150138464	AG09309	skin:	n/a
20	chr3:150138414-150138464	BJ	skin:	n/a
21	chr3:150138414-150138464	PANC-1	pancreas:	n/a
22	chr3:150138414-150138464	Jurkat	blood:	n/a
23	chr3:150138414-150138464	LNCaP	prostate:	n/a
24	chr3:150138414-150138464	SK-N-SH	brain:	n/a
25	chr3:150138414-150138464	GM12892	blood:	n/a
26	chr3:150138414-150138464	NHBE	bronchial:	n/a
27	chr3:150138414-150138464	NB4	blood:	n/a
28	chr3:150138414-150138464	A549	lung:	n/a
29	chr3:150138414-150138464	HRPEpiC	eye:	n/a
30	chr3:150138414-150138464	AG04449	skin:	fetal
31	chr3:150138414-150138464	GM12891	blood:	n/a
32	chr3:150138414-150138464	H1-hESC	embryonic stem cell:	embryo
33	chr3:150138414-150138464	HRCEpiC	kidney:	n/a
34	chr3:150138414-150138464	HAEpiC	amniotic membrane:	n/a
35	chr3:150138414-150138464	AG04450	lung:	fetal
36	chr3:150138414-150138464	MCF10A-Er-Src	breast:	n/a
37	chr3:150138414-150138464	GM12878	blood:	n/a
38	chr3:150138414-150138464	HRE	kidney:	n/a
39	chr3:150138414-150138464	NT2-D1	testis:	n/a
40	chr3:150138414-150138464	HCF	heart:	n/a
41	chr3:150138414-150138464	HEEpiC	esophagus:	n/a
42	chr3:150138414-150138464	PFSK-1	brain:	n/a
43	chr3:150138414-150138464	HCT-116	colon:	n/a
44	chr3:150138414-150138464	CMK	blood:	n/a
45	chr3:150138414-150138464	GM06990	blood:	n/a
46	chr3:150138414-150138464	SK-N-SH_RA	brain:	n/a
47	chr3:150138414-150138464	HL-60	blood:	n/a
48	chr3:150138414-150138464	K562	blood:	n/a
49	chr3:150138414-150138464	SAEC	small airway:	n/a
50	chr3:150138414-150138464	ProgFib	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150086902..150089689-chr3:150137707..150139758,2	MCF-7	breast:
2	chr3:149956495..149958158-chr3:150137988..150139629,2	MCF-7	breast:
3	chr3:150134899..150136679-chr3:150137562..150139549,2	MCF-7	breast:
4	chr3:150091318..150093525-chr3:150137664..150139823,2	K562	blood:

No data

Variant related genes	Relation type
TSC22D2	TF binding region
TSC22D2	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10513374	0.81[JPT][hapmap]
rs10935800	0.81[JPT][hapmap]
rs11706245	0.81[ASN][1000 genomes]
rs11711035	0.82[ASN][1000 genomes]
rs12639090	0.81[JPT][hapmap]
rs13080841	0.82[ASN][1000 genomes]
rs13080858	0.82[ASN][1000 genomes]
rs13082720	0.99[ASN][1000 genomes]
rs13099758	0.80[ASN][1000 genomes]
rs1450335	0.99[ASN][1000 genomes]
rs1450336	0.99[ASN][1000 genomes]
rs1450344	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16862651	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868672	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868673	1.00[CEU][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2167177	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28514580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2868425	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs34173517	0.80[ASN][1000 genomes]
rs4423794	0.81[JPT][hapmap]
rs4681206	0.82[ASN][1000 genomes]
rs4681615	0.99[ASN][1000 genomes]
rs4681618	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs4681619	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762432	0.83[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6770424	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7427177	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7626725	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7651353	0.91[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7651989	0.83[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9289810	0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs9784281	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784335	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9813752	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826729	0.81[JPT][hapmap]
rs9846873	0.99[ASN][1000 genomes]
rs9882777	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1799287	chr3:150125721-150147118	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150131000-150138600	Weak transcription	Lung	lung
2	chr3:150131000-150152000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:150131000-150166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:150131200-150138600	Enhancers	Colon Smooth Muscle	Colon
5	chr3:150131400-150138600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:150132200-150140600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:150132400-150139200	Weak transcription	Fetal Stomach	stomach
8	chr3:150132400-150146000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:150132400-150151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:150132400-150151600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:150132400-150159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:150132400-150160400	Weak transcription	Pancreas	Pancrea
13	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
15	chr3:150132600-150145200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:150132800-150145800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:150132800-150145800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:150132800-150151000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:150133000-150139800	Weak transcription	Fetal Kidney	kidney
20	chr3:150133600-150139600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:150133600-150139800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:150133600-150151000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:150133600-150159200	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:150133600-150159200	Weak transcription	Left Ventricle	heart
25	chr3:150133800-150159200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:150134000-150138600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:150134000-150143000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:150134000-150143800	Weak transcription	Aorta	Aorta
29	chr3:150134000-150146000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:150134000-150147000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:150134000-150159200	Weak transcription	Thymus	Thymus
32	chr3:150134200-150139200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:150134200-150140800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:150134400-150138600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:150134400-150139200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:150134600-150146000	Weak transcription	Stomach Mucosa	stomach
37	chr3:150134600-150174800	Weak transcription	Dnd41	blood
38	chr3:150134800-150139800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:150135000-150139200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:150135600-150145600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:150136000-150140800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:150136000-150144000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:150136000-150145800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:150136000-150160800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:150136200-150139600	Weak transcription	Ovary	ovary
47	chr3:150136200-150139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:150136200-150140200	Enhancers	NHEK	skin
49	chr3:150136200-150140600	Weak transcription	Fetal Brain Female	brain
50	chr3:150136200-150142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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