Variant report

Variant	rs193442
Chromosome Location	chr14:71820434-71820435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12878009	0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12897119	0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs193440	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs193441	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193443	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36535	0.82[AMR][1000 genomes]
rs41217	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41218	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41219	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41220	0.83[ASW][hapmap];0.80[YRI][hapmap]
rs41224	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41225	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41227	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41229	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4464023	0.90[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap]
rs7153726	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8007271	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8007521	0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8016217	0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs8023058	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917391	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv1831401	chr14:71786411-71845264	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs193442	SIPA1L1	cis	parietal	SCAN
rs193442	VSX2	cis	parietal	SCAN
rs193442	SLC8A3	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71795000-71821800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr14:71795200-71821600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr14:71795800-71821400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:71797200-71821800	Weak transcription	HSMMtube	muscle
5	chr14:71797600-71821200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:71800600-71822200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr14:71801400-71821000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:71805200-71822200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:71805400-71828600	Weak transcription	Dnd41	blood
10	chr14:71806600-71838400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr14:71807000-71821600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr14:71807600-71822000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:71808200-71822200	Weak transcription	Fetal Intestine Small	intestine
14	chr14:71808400-71822000	Weak transcription	Small Intestine	intestine
15	chr14:71808400-71829800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:71808600-71821400	Weak transcription	Primary B cells from cord blood	blood
17	chr14:71808600-71821600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:71808800-71838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr14:71810600-71822400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr14:71810800-71822200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr14:71812000-71821600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr14:71812000-71821800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr14:71812200-71821200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr14:71812200-71821600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:71812200-71821600	Weak transcription	Ovary	ovary
26	chr14:71812200-71822600	Weak transcription	Esophagus	oesophagus
27	chr14:71812200-71838800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr14:71813200-71822000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr14:71813400-71829000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr14:71813600-71821600	Weak transcription	Liver	Liver
31	chr14:71813600-71822800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr14:71814200-71821400	Weak transcription	NHLF	lung
33	chr14:71816200-71821600	Weak transcription	Colon Smooth Muscle	Colon
34	chr14:71816200-71827800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr14:71816600-71820800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr14:71816600-71826800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr14:71816800-71821000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr14:71816800-71821400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr14:71816800-71822600	Weak transcription	Fetal Muscle Leg	muscle
40	chr14:71817000-71821600	Weak transcription	Right Atrium	heart
41	chr14:71817200-71821200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:71817200-71821200	Weak transcription	Fetal Stomach	stomach
43	chr14:71818200-71821200	Weak transcription	Osteobl	bone
44	chr14:71818200-71821600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:71818200-71822200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr14:71818400-71821000	ZNF genes & repeats	GM12878-XiMat	blood
47	chr14:71818400-71821400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr14:71818400-71821600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:71818400-71821600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr14:71818800-71821800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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