Variant report

Variant	rs72954410
Chromosome Location	chr3:112116518-112116519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTLA-1	chr3:112115494-112116995	ENSG00000243081

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs57306336	1.00[AMR][1000 genomes]
rs72952422	1.00[AMR][1000 genomes]
rs72952484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649698	1.00[AMR][1000 genomes]
rs7649901	1.00[AMR][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	nsv877341	chr3:112079277-112125521	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1002567	chr3:112088498-112144063	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2830128	chr3:112090292-112144026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv997659	chr3:112099148-112135687	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv998316	chr3:112102565-112116643	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112107200-112117000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr3:112107400-112117000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:112110600-112116600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:112110800-112118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112111400-112120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:112111800-112125400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:112112400-112116600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:112112400-112118000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:112112800-112116800	Enhancers	Fetal Lung	lung
10	chr3:112112800-112117000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:112113000-112116600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:112113200-112117000	Enhancers	Placenta	Placenta
13	chr3:112113400-112116600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:112113400-112117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:112113400-112124600	Weak transcription	HMEC	breast
16	chr3:112113600-112116600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:112113600-112120600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:112114000-112116600	Weak transcription	Lung	lung
19	chr3:112114400-112116800	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:112114600-112116600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:112114600-112116600	Weak transcription	Aorta	Aorta
22	chr3:112115000-112121200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:112115200-112116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:112115200-112118000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:112115200-112127600	Weak transcription	Fetal Kidney	kidney
26	chr3:112115400-112116600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:112115600-112116600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:112116400-112116600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:112116400-112116800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:112116400-112116800	Enhancers	Ovary	ovary
31	chr3:112116400-112116800	Enhancers	Right Atrium	heart
32	chr3:112116400-112116800	Enhancers	HUVEC	blood vessel
33	chr3:112116400-112117000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:112116400-112117000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112116400-112117000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:112116400-112117000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:112116400-112117000	Enhancers	Adipose Nuclei	Adipose
38	chr3:112116400-112118000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:112116400-112118000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:112116400-112118200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:112116400-112118400	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:112116400-112126800	Enhancers	HUES64 Cell Line	embryonic stem cell

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