Variant report

Variant	rs7688715
Chromosome Location	chr4:3342137-3342138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3342111-3342161	BJ	skin:	n/a
2	chr4:3342111-3342161	T-47D	breast:	n/a
3	chr4:3342111-3342161	ECC-1	luminal epithelium:	n/a
4	chr4:3342111-3342161	HRE	kidney:	n/a
5	chr4:3342111-3342161	PANC-1	pancreas:	n/a
6	chr4:3342111-3342161	HL-60	blood:	n/a
7	chr4:3342111-3342161	HAEpiC	amniotic membrane:	n/a
8	chr4:3342111-3342161	PrEC	prostate:	n/a
9	chr4:3342111-3342161	HepG2	liver:	n/a
10	chr4:3342111-3342161	SKMC	muscle:	n/a
11	chr4:3342111-3342161	SAEC	small airway:	n/a
12	chr4:3342111-3342161	RPTEC	kidney:	n/a
13	chr4:3342111-3342161	GM19239	blood:	n/a
14	chr4:3342111-3342161	HRPEpiC	eye:	n/a
15	chr4:3342111-3342161	GM12891	blood:	n/a
16	chr4:3342111-3342161	HIPEpiC	eye:	n/a
17	chr4:3342111-3342161	AG09319	gingival:	n/a
18	chr4:3342111-3342161	MCF-7	breast:	n/a
19	chr4:3342111-3342161	CMK	blood:	n/a
20	chr4:3342111-3342161	GM12892	blood:	n/a
21	chr4:3342111-3342161	NHDF-neo	bronchial:	n/a
22	chr4:3342111-3342161	SK-N-MC	brain:	n/a
23	chr4:3342111-3342161	BE2_C	brain:	n/a
24	chr4:3342111-3342161	HCM	heart:	n/a
25	chr4:3342111-3342161	HCPEpiC	choroid plexus:	n/a
26	chr4:3342111-3342161	H1-hESC	embryonic stem cell:	embryo
27	chr4:3342111-3342161	NB4	blood:	n/a
28	chr4:3342111-3342161	ovcar-3	ovarian:	n/a
29	chr4:3342111-3342161	HPAEpiC	pulmonary alveolar:	n/a
30	chr4:3342111-3342161	Hela-S3	cervix:	n/a
31	chr4:3342111-3342161	SK-N-SH_RA	brain:	n/a
32	chr4:3342111-3342161	Jurkat	blood:	n/a
33	chr4:3342111-3342161	ProgFib	skin:	n/a
34	chr4:3342111-3342161	HUVEC	blood vessel:	n/a
35	chr4:3342111-3342161	GM06990	blood:	n/a
36	chr4:3342111-3342161	IMR90	lung:	fetal
37	chr4:3342111-3342161	AG04449	skin:	fetal
38	chr4:3342111-3342161	NT2-D1	testis:	n/a
39	chr4:3342111-3342161	HEEpiC	esophagus:	n/a
40	chr4:3342111-3342161	AG10803	skin:	n/a
41	chr4:3342111-3342161	HEK293	kidney:	embryo
42	chr4:3342111-3342161	HNPCEpiC	eye:	n/a
43	chr4:3342111-3342161	Caco-2	colon:	n/a
44	chr4:3342111-3342161	HMEC	breast:	n/a
45	chr4:3342111-3342161	AoSMC	blood vessel:	n/a
46	chr4:3342111-3342161	HRCEpiC	kidney:	n/a
47	chr4:3342111-3342161	K562	blood:	n/a
48	chr4:3342111-3342161	LNCaP	prostate:	n/a
49	chr4:3342111-3342161	U87	brain:	n/a
50	chr4:3342111-3342161	Hepatocyte	liver:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3338818..3342772-chr4:3461368..3467187,7	MCF-7	breast:
2	chr4:3338889..3343165-chr4:3463099..3467145,4	MCF-7	breast:
3	chr4:3340754..3343218-chr4:3436055..3438880,2	MCF-7	breast:
4	chr4:3330743..3332280-chr4:3339908..3342252,2	MCF-7	breast:
5	chr4:3292758..3295748-chr4:3341243..3344299,3	MCF-7	breast:
6	chr4:3341846..3343634-chr4:3447069..3448712,2	MCF-7	breast:

No data

Variant related genes	Relation type
RGS12	CpG island
ENSG00000175920	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13126960	0.81[AMR][1000 genomes]
rs16844106	1.00[MEX][hapmap]
rs17804577	0.83[TSI][hapmap]
rs6822719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6826787	0.81[LWK][hapmap]
rs6837479	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7660068	0.88[EUR][1000 genomes]
rs7678857	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs7680197	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs7687590	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	esv1803957	chr4:3339038-3343475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv1837613	chr4:3339038-3343475	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv3398851	chr4:3341979-3344927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv593443	chr4:3342137-3343418	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv593444	chr4:3342137-3343475	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv593445	chr4:3342137-3344891	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv593446	chr4:3342137-3346617	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:3320000-3344000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
5	chr4:3321000-3347000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:3323600-3344000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:3323600-3344800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:3324000-3343600	Weak transcription	HSMM	muscle
9	chr4:3324200-3342600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:3324200-3343600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:3325200-3342800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:3325600-3348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:3326200-3342800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:3326400-3343600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:3326400-3343600	Weak transcription	NHLF	lung
16	chr4:3326400-3343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:3326400-3344800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:3326400-3348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:3328400-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:3330200-3343600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:3331000-3343600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:3331400-3342400	Weak transcription	Psoas Muscle	Psoas
23	chr4:3332400-3343800	Weak transcription	Fetal Intestine Small	intestine
24	chr4:3332600-3342600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:3332800-3343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:3332800-3343600	Weak transcription	Primary T cells from cord blood	blood
27	chr4:3332800-3343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:3334000-3342200	Weak transcription	Pancreas	Pancrea
29	chr4:3334000-3342400	Weak transcription	Left Ventricle	heart
30	chr4:3334000-3345800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
32	chr4:3334400-3343600	Weak transcription	Adipose Nuclei	Adipose
33	chr4:3334600-3343600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:3337000-3344000	Weak transcription	Fetal Kidney	kidney
35	chr4:3337400-3343600	Weak transcription	Ovary	ovary
36	chr4:3337400-3343600	Weak transcription	Right Ventricle	heart
37	chr4:3337600-3343600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:3338200-3343600	Weak transcription	Brain Anterior Caudate	brain
39	chr4:3338400-3343600	Weak transcription	HepG2	liver
40	chr4:3338400-3343800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr4:3339200-3353200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:3339800-3343600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:3339800-3343600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:3340200-3343200	Enhancers	Lung	lung
45	chr4:3340200-3344000	Enhancers	Brain Germinal Matrix	brain
46	chr4:3340400-3342600	Weak transcription	A549	lung
47	chr4:3340400-3343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:3340600-3342200	Weak transcription	Spleen	Spleen
49	chr4:3340600-3342400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:3340600-3343600	Weak transcription	Placenta	Placenta

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