Variant report

Variant	rs17419936
Chromosome Location	chr1:158013048-158013049
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD5L-1	chr1:158012874-158013169	l_138_chr1:158012873-158014999_colon

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10796989	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs10796990	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs10796991	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs10796993	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs10908613	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs10908614	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]
rs11264879	0.89[CEU][hapmap];0.96[GIH][hapmap]
rs11580742	1.00[CHD][hapmap]
rs11585913	1.00[CHD][hapmap]
rs16839658	0.89[CEU][hapmap]
rs17419999	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17453741	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1925033	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs4971122	0.88[CEU][hapmap]
rs6427417	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs6686246	0.89[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17419936	C1orf92	cis	parietal	SCAN
rs17419936	VPS39	trans	parietal	SCAN
rs17419936	ASH1L	cis	cerebellum	SCAN
rs17419936	DCST1	cis	cerebellum	SCAN
rs17419936	GATAD2B	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157997600-158047600	Weak transcription	Dnd41	blood
2	chr1:158001200-158047400	Weak transcription	Thymus	Thymus
3	chr1:158002400-158025400	Weak transcription	Fetal Brain Female	brain
4	chr1:158008000-158014800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:158008000-158019600	Weak transcription	Colonic Mucosa	Colon
6	chr1:158008200-158015000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:158008200-158018400	Weak transcription	Spleen	Spleen
8	chr1:158008200-158023000	Weak transcription	A549	lung
9	chr1:158008200-158024600	Weak transcription	Placenta	Placenta
10	chr1:158008800-158013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:158008800-158015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:158009200-158013200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:158009200-158013600	Weak transcription	Fetal Kidney	kidney
14	chr1:158009400-158013400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:158009400-158014800	Weak transcription	Left Ventricle	heart
16	chr1:158009400-158024400	Weak transcription	Hela-S3	cervix
17	chr1:158009600-158013200	Weak transcription	NH-A	brain
18	chr1:158009600-158013400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:158009600-158022600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:158010000-158014600	Weak transcription	NHDF-Ad	bronchial
21	chr1:158010000-158015000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:158010000-158015000	Weak transcription	HSMMtube	muscle
23	chr1:158010000-158015200	Weak transcription	HUVEC	blood vessel
24	chr1:158010000-158023000	Weak transcription	HSMM	muscle
25	chr1:158010200-158013200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:158010200-158014600	Weak transcription	Osteobl	bone
27	chr1:158010200-158020600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:158011000-158013800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:158011000-158015400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:158011000-158017200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:158011200-158014800	Weak transcription	HMEC	breast
32	chr1:158011400-158013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:158011400-158014200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:158011800-158013600	Enhancers	Fetal Intestine Small	intestine
35	chr1:158012000-158013400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:158012200-158013200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:158012200-158019800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:158012400-158013400	Weak transcription	Psoas Muscle	Psoas
39	chr1:158012400-158013800	Weak transcription	NHEK	skin
40	chr1:158012400-158014000	Enhancers	Rectal Smooth Muscle	rectum
41	chr1:158012400-158017200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:158012600-158014800	Weak transcription	NHLF	lung
43	chr1:158012600-158015200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:158012800-158013200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:158012800-158013400	Enhancers	Aorta	Aorta
46	chr1:158012800-158013400	Enhancers	Fetal Heart	heart
47	chr1:158012800-158013400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:158012800-158013600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:158012800-158015800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:158012800-158016800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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