Variant report

Variant	rs60949597
Chromosome Location	chr3:112116817-112116818
allele	A/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: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[ASN][1000 genomes]
rs10934164	1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11712849	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	1.00[ASN][1000 genomes]
rs12497979	1.00[ASN][1000 genomes]
rs13084103	1.00[ASN][1000 genomes]
rs1317295	1.00[ASN][1000 genomes]
rs1317658	1.00[ASN][1000 genomes]
rs13316383	1.00[ASN][1000 genomes]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[ASN][1000 genomes]
rs2633546	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683891	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683892	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615303	1.00[ASN][1000 genomes]
rs4507229	1.00[ASN][1000 genomes]
rs4622877	1.00[ASN][1000 genomes]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	1.00[ASN][1000 genomes]
rs56008438	1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262459	1.00[ASN][1000 genomes]
rs62264125	1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	1.00[ASN][1000 genomes]
rs62278768	1.00[ASN][1000 genomes]
rs62278769	1.00[ASN][1000 genomes]
rs62278770	1.00[ASN][1000 genomes]
rs62278771	1.00[ASN][1000 genomes]
rs62278843	1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6775536	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795820	1.00[ASN][1000 genomes]
rs73223638	1.00[ASN][1000 genomes]
rs7609904	1.00[ASN][1000 genomes]
rs7612748	1.00[ASN][1000 genomes]
rs7621431	1.00[ASN][1000 genomes]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[ASN][1000 genomes]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9810421	1.00[ASN][1000 genomes]
rs9816969	1.00[ASN][1000 genomes]
rs9818407	1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	1.00[ASN][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	1.00[ASN][1000 genomes]
rs9855755	1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:34 , 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	chr3:112110800-112118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:112111400-112120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:112111800-112125400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:112112400-112118000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:112112800-112117000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:112113200-112117000	Enhancers	Placenta	Placenta
9	chr3:112113400-112117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:112113400-112124600	Weak transcription	HMEC	breast
11	chr3:112113600-112120600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:112115000-112121200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112115200-112118000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112115200-112127600	Weak transcription	Fetal Kidney	kidney
15	chr3:112116400-112117000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:112116400-112117000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112116400-112117000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:112116400-112117000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:112116400-112117000	Enhancers	Adipose Nuclei	Adipose
20	chr3:112116400-112118000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:112116400-112118000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:112116400-112118200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:112116400-112118400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:112116400-112126800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr3:112116600-112117000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr3:112116600-112117000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:112116600-112117000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:112116600-112117000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:112116600-112117000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:112116600-112117000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:112116600-112117000	Enhancers	Aorta	Aorta
32	chr3:112116600-112119800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:112116600-112121200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:112116800-112117600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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