Variant report

Variant	rs16968897
Chromosome Location	chr15:77825298-77825299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77824813..77828626-chr15:77832957..77835709,3	K562	blood:
2	chr15:77822210..77823977-chr15:77824433..77827126,2	MCF-7	breast:
3	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
4	chr15:77819703..77822055-chr15:77824303..77826129,2	MCF-7	breast:
5	chr15:77318006..77320545-chr15:77823819..77825368,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-1	chr15:77823445-77826452	ENSG00000259362.2

No data

Variant related genes	Relation type
ENSG00000140368	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11855272	0.81[EUR][1000 genomes]
rs11856084	0.90[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11858844	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12324795	0.91[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1317320	0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs16953967	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968893	0.84[ASN][1000 genomes]
rs16968895	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16968900	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968930	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17385296	0.91[CEU][hapmap]
rs17394448	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs17471431	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17471480	0.85[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17471697	0.90[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs17471753	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17472200	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2012740	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2012756	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2137111	1.00[JPT][hapmap]
rs2307141	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2864840	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2867303	0.83[ASN][1000 genomes]
rs3784788	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4243046	0.81[EUR][1000 genomes]
rs4886870	0.80[ASN][1000 genomes]
rs4886874	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56097641	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59204923	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59362734	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59386622	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61097729	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61306472	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61483316	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74026910	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs74026912	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs74026913	0.82[EUR][1000 genomes]
rs74026918	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs74026923	0.84[EUR][1000 genomes]
rs74026925	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74026926	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74026930	0.84[ASN][1000 genomes]
rs74026931	0.84[ASN][1000 genomes]
rs74026932	0.84[ASN][1000 genomes]
rs74026933	0.84[ASN][1000 genomes]
rs7495653	1.00[ASN][1000 genomes]
rs869302	0.93[ASN][1000 genomes]
rs869310	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs907370	0.80[EUR][1000 genomes]
rs907371	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs907387	0.84[ASN][1000 genomes]
rs907398	0.91[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS 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	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16968897	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77819600-77828600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:77819800-77831000	Weak transcription	Gastric	stomach
3	chr15:77820800-77826200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:77821000-77825600	Weak transcription	Fetal Brain Female	brain
5	chr15:77821000-77825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:77821000-77825800	Enhancers	Spleen	Spleen
7	chr15:77821000-77826800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
9	chr15:77821400-77826000	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:77821600-77825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:77821600-77825400	Weak transcription	Fetal Brain Male	brain
12	chr15:77821600-77826000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:77821600-77830200	Weak transcription	Left Ventricle	heart
14	chr15:77821800-77827600	Weak transcription	Pancreas	Pancrea
15	chr15:77822000-77825400	Weak transcription	Right Ventricle	heart
16	chr15:77822000-77825600	Weak transcription	Fetal Heart	heart
17	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
18	chr15:77822400-77825400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:77822400-77825400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:77822400-77825400	Weak transcription	Fetal Lung	lung
21	chr15:77822400-77825600	Weak transcription	Ovary	ovary
22	chr15:77822600-77825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:77823400-77825800	Weak transcription	Fetal Intestine Large	intestine
24	chr15:77823400-77826600	Weak transcription	Fetal Intestine Small	intestine
25	chr15:77823600-77827200	Enhancers	Fetal Stomach	stomach
26	chr15:77824000-77825400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:77824000-77826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:77824200-77825400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:77824200-77825600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:77824600-77825800	Weak transcription	HepG2	liver
31	chr15:77824800-77829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:77825000-77827000	Enhancers	Fetal Kidney	kidney
33	chr15:77825200-77825600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:77825200-77825800	Enhancers	Stomach Mucosa	stomach
35	chr15:77825200-77826000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:77825200-77826000	Enhancers	Brain Germinal Matrix	brain
37	chr15:77825200-77827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:77825200-77827000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr15:77825200-77827000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:77825200-77827200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr15:77825200-77827200	Enhancers	Placenta	Placenta
42	chr15:77825200-77827800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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