Variant report

Variant	rs3923950
Chromosome Location	chr1:212811875-212811876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212731680..212733732-chr1:212810239..212812823,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BATF3-2	chr1:212810445-212811889	XLOC_001195
2	lnc-BATF3-2	chr1:212811656-212811902	XLOC_001195

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11119990	0.92[ASN][1000 genomes]
rs12143644	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17019532	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17019541	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1876410	0.94[ASN][1000 genomes]
rs2501842	0.93[JPT][hapmap]
rs3122716	0.93[JPT][hapmap]
rs3123541	0.86[JPT][hapmap]
rs3125300	0.93[JPT][hapmap]
rs3125301	0.93[JPT][hapmap]
rs61830699	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3923950	CTSC	trans	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212794400-212812200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
3	chr1:212807800-212812600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:212807800-212812800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:212808000-212812600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:212808200-212812800	Enhancers	Fetal Stomach	stomach
7	chr1:212808200-212813000	Enhancers	Fetal Heart	heart
8	chr1:212808200-212813000	Enhancers	Fetal Thymus	thymus
9	chr1:212808400-212812600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:212808600-212813000	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:212808800-212812600	Enhancers	Right Ventricle	heart
12	chr1:212808800-212812800	Enhancers	Placenta	Placenta
13	chr1:212809400-212812600	Enhancers	Fetal Brain Male	brain
14	chr1:212810000-212812400	Enhancers	Fetal Lung	lung
15	chr1:212810200-212812800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:212810200-212812800	Enhancers	Thymus	Thymus
17	chr1:212810400-212812600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:212810600-212812400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:212810600-212812400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:212810600-212812400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:212810600-212812600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:212810600-212813200	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:212810800-212812200	Enhancers	Dnd41	blood
24	chr1:212810800-212812400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:212810800-212812400	Weak transcription	Lung	lung
26	chr1:212810800-212812400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:212810800-212813000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:212810800-212813000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:212810800-212813000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:212810800-212813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:212810800-212813800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:212811000-212816800	Weak transcription	Fetal Intestine Large	intestine
33	chr1:212811200-212812000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:212811200-212812000	Flanking Active TSS	Osteobl	bone
35	chr1:212811200-212812200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:212811200-212812400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:212811400-212812000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr1:212811400-212812200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:212811400-212812200	Flanking Active TSS	NH-A	brain
40	chr1:212811400-212812400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:212811400-212812400	Enhancers	Brain Anterior Caudate	brain
42	chr1:212811400-212812600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr1:212811400-212812800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:212811600-212812000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:212811600-212812000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr1:212811600-212812000	Flanking Active TSS	NHLF	lung
47	chr1:212811600-212812200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:212811600-212812400	Enhancers	Fetal Brain Female	brain
49	chr1:212811600-212812600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr1:212811600-212812600	Enhancers	Colon Smooth Muscle	Colon

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