Variant report

Variant	rs3749952
Chromosome Location	chr6:31683157-31683158
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:183)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31683131-31683181	GM12892	blood:	n/a
2	chr6:31683120-31683170	A549	lung:	n/a
3	chr6:31683131-31683181	MCF10A-Er-Src	breast:	n/a
4	chr6:31683131-31683181	NB4	blood:	n/a
5	chr6:31683109-31683159	NT2-D1	testis:	n/a
6	chr6:31683120-31683170	NHBE	bronchial:	n/a
7	chr6:31683131-31683181	PANC-1	pancreas:	n/a
8	chr6:31683109-31683159	IMR90	lung:	fetal
9	chr6:31683109-31683159	NB4	blood:	n/a
10	chr6:31683109-31683159	AoSMC	blood vessel:	n/a
11	chr6:31683109-31683159	ECC-1	luminal epithelium:	n/a
12	chr6:31683109-31683159	NH-A	brain:	n/a
13	chr6:31683131-31683181	SKMC	muscle:	n/a
14	chr6:31683120-31683170	HL-60	blood:	n/a
15	chr6:31683120-31683170	HRCEpiC	kidney:	n/a
16	chr6:31683131-31683181	ovcar-3	ovarian:	n/a
17	chr6:31683120-31683170	T-47D	breast:	n/a
18	chr6:31683109-31683159	CMK	blood:	n/a
19	chr6:31683120-31683170	SK-N-MC	brain:	n/a
20	chr6:31683109-31683159	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:31683120-31683170	BE2_C	brain:	n/a
22	chr6:31683120-31683170	HEEpiC	esophagus:	n/a
23	chr6:31683120-31683170	HIPEpiC	eye:	n/a
24	chr6:31683120-31683170	PrEC	prostate:	n/a
25	chr6:31683131-31683181	SK-N-MC	brain:	n/a
26	chr6:31683131-31683181	SK-N-SH	brain:	n/a
27	chr6:31683109-31683159	HL-60	blood:	n/a
28	chr6:31683120-31683170	AoSMC	blood vessel:	n/a
29	chr6:31683131-31683181	MCF-7	breast:	n/a
30	chr6:31683131-31683181	BE2_C	brain:	n/a
31	chr6:31683109-31683159	AG09309	skin:	n/a
32	chr6:31683109-31683159	GM12892	blood:	n/a
33	chr6:31683120-31683170	NT2-D1	testis:	n/a
34	chr6:31683120-31683170	HCT-116	colon:	n/a
35	chr6:31683109-31683159	BJ	skin:	n/a
36	chr6:31683131-31683181	RPTEC	kidney:	n/a
37	chr6:31683131-31683181	HUVEC	blood vessel:	n/a
38	chr6:31683131-31683181	NH-A	brain:	n/a
39	chr6:31683109-31683159	RPTEC	kidney:	n/a
40	chr6:31683109-31683159	U87	brain:	n/a
41	chr6:31683109-31683159	PANC-1	pancreas:	n/a
42	chr6:31683120-31683170	NHDF-neo	bronchial:	n/a
43	chr6:31683109-31683159	SAEC	small airway:	n/a
44	chr6:31683120-31683170	GM12891	blood:	n/a
45	chr6:31683109-31683159	PrEC	prostate:	n/a
46	chr6:31683109-31683159	Caco-2	colon:	n/a
47	chr6:31683131-31683181	H1-hESC	embryonic stem cell:	embryo
48	chr6:31683109-31683159	AG04449	skin:	fetal
49	chr6:31683120-31683170	HMEC	breast:	n/a
50	chr6:31683109-31683159	MCF-7	breast:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LY6G6D-1	chr6:31683133-31683401	NONHSAT108823

No data

Variant related genes	Relation type
ENSG00000204422	CpG island
LY6G6E	CpG island
C6orf25	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12177823	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075787	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255741	0.81[ASN][1000 genomes]
rs2736158	0.83[ASN][1000 genomes]
rs2736161	0.86[ASN][1000 genomes]
rs2736163	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736165	0.85[ASN][1000 genomes]
rs2736182	0.85[ASN][1000 genomes]
rs2857696	0.81[ASN][1000 genomes]
rs4713479	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805258	0.86[ASN][1000 genomes]
rs805264	0.86[ASN][1000 genomes]
rs805266	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805267	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805268	0.86[ASN][1000 genomes]
rs805269	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805270	0.86[ASN][1000 genomes]
rs805272	0.86[ASN][1000 genomes]
rs805283	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805291	0.93[ASN][1000 genomes]
rs805295	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805298	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805300	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296001	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461717	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461718	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461719	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9461721	0.89[EUR][1000 genomes]
rs9469040	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9469046	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
2	chr6:31672000-31685400	Weak transcription	Gastric	stomach
3	chr6:31677600-31683600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:31678400-31683200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:31678400-31684200	Enhancers	Fetal Brain Male	brain
6	chr6:31679200-31683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:31679200-31687800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:31679400-31691200	Weak transcription	Primary B cells from cord blood	blood
9	chr6:31680000-31683600	Enhancers	Fetal Thymus	thymus
10	chr6:31680200-31685200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:31680400-31683200	Enhancers	Fetal Intestine Large	intestine
12	chr6:31680400-31683400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:31680400-31685400	Weak transcription	Pancreas	Pancrea
14	chr6:31680800-31685200	Weak transcription	NHEK	skin
15	chr6:31681200-31683200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:31681200-31683600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:31681400-31683600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:31681400-31683600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:31681400-31683800	Enhancers	Fetal Muscle Leg	muscle
20	chr6:31681600-31683400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:31681600-31683600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:31681600-31683600	Enhancers	Esophagus	oesophagus
23	chr6:31681600-31683600	Enhancers	Placenta	Placenta
24	chr6:31681600-31683800	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:31681600-31684000	Enhancers	Fetal Lung	lung
26	chr6:31681800-31683400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:31681800-31683800	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:31682000-31685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:31682000-31685400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:31682000-31692800	Weak transcription	HSMMtube	muscle
31	chr6:31682000-31693800	Weak transcription	Fetal Kidney	kidney
32	chr6:31682200-31683600	Enhancers	Brain Germinal Matrix	brain
33	chr6:31682200-31683600	Enhancers	Colon Smooth Muscle	Colon
34	chr6:31682200-31683600	Enhancers	Fetal Stomach	stomach
35	chr6:31682200-31685200	Weak transcription	Colonic Mucosa	Colon
36	chr6:31682200-31685200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:31682200-31685600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:31682200-31685800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:31682200-31693400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:31682400-31685000	Weak transcription	K562	blood
41	chr6:31682400-31685200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:31682400-31685200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:31682400-31685200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:31682400-31685200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:31682400-31685200	Weak transcription	Stomach Mucosa	stomach
46	chr6:31682400-31692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:31682400-31693600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:31682400-31693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:31682400-31696400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:31682800-31683200	Enhancers	Rectal Smooth Muscle	rectum

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