Variant report

Variant	rs3803383
Chromosome Location	chr15:83423493-83423494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83417813..83422044-chr15:83423321..83428058,7	MCF-7	breast:
2	chr15:83423255..83426158-chr15:83477607..83479598,3	MCF-7	breast:
3	chr15:83417361..83424147-chr15:83476165..83481050,26	MCF-7	breast:
4	chr15:83422950..83425938-chr15:83474104..83476004,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WHAMM-2	chr15:83421636-83425960	ENSG00000252690.2

Variant related genes	Relation type
ENSG00000156232	Chromatin interaction
ENSG00000252690	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000186628	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1124911	0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28540813	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28664062	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28847707	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638544	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779062	0.83[ASN][1000 genomes]
rs7174656	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023873	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3803383	RASGRF1	cis	parietal	SCAN
rs3803383	CTSH	cis	parietal	SCAN
rs3803383	HDGFRP3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83420000-83426600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:83420200-83427000	Weak transcription	Gastric	stomach
3	chr15:83420200-83433400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:83420400-83424400	Weak transcription	Fetal Heart	heart
5	chr15:83420400-83427000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:83420400-83427000	Weak transcription	Esophagus	oesophagus
7	chr15:83420400-83436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:83420600-83423800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:83420600-83424000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:83420600-83426400	Weak transcription	Thymus	Thymus
11	chr15:83420600-83429000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:83420800-83423600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:83420800-83423600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:83420800-83427000	Weak transcription	Aorta	Aorta
15	chr15:83420800-83427000	Weak transcription	Right Ventricle	heart
16	chr15:83420800-83431400	Weak transcription	Stomach Mucosa	stomach
17	chr15:83421000-83424000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:83421000-83428000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:83421000-83428200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:83421000-83428400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:83421000-83428400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:83421000-83428600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:83421000-83429400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:83421200-83423600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:83421200-83423600	Weak transcription	Brain Angular Gyrus	brain
26	chr15:83421200-83424600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
27	chr15:83421200-83425200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:83421200-83426000	Strong transcription	K562	blood
29	chr15:83421200-83426600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:83421200-83428200	Strong transcription	Fetal Thymus	thymus
31	chr15:83421200-83430000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr15:83421200-83431200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:83421200-83431200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:83421200-83431600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:83421200-83432000	Strong transcription	A549	lung
36	chr15:83421400-83423600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:83421400-83426600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr15:83421400-83427000	Weak transcription	Pancreas	Pancrea
39	chr15:83421400-83428200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:83421400-83428200	Strong transcription	HUVEC	blood vessel
41	chr15:83421400-83428400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr15:83421400-83431400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:83421400-83431600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:83421600-83428200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:83421600-83431200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:83421600-83431600	Strong transcription	Adipose Nuclei	Adipose
47	chr15:83421600-83432800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:83421800-83425400	Strong transcription	Brain Germinal Matrix	brain
49	chr15:83421800-83427600	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:83422000-83424200	Weak transcription	Psoas Muscle	Psoas

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