Variant report

Variant	rs3123536
Chromosome Location	chr1:212809606-212809607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212808458..212810460-chr1:212812448..212814204,2	K562	blood:
2	chr1:212806678..212809616-chr1:212824409..212825963,2	MCF-7	breast:
3	chr1:212803388..212806406-chr1:212807371..212811389,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BATF3-2	chr1:212808800-212810008	XLOC_001195
2	lnc-BATF3-2	chr1:212805714-212810008	XLOC_001195

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2501840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501841	0.86[ASN][1000 genomes]
rs3123535	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3123539	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3890801	0.90[CEU][hapmap]
rs6656504	0.90[CEU][hapmap]
rs6682816	0.82[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3123536	KCNH1	cis	parietal	SCAN
rs3123536	VASH2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212793600-212810600	Weak transcription	Esophagus	oesophagus
2	chr1:212794400-212812200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
4	chr1:212805000-212810400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:212807800-212811000	Enhancers	Fetal Intestine Large	intestine
6	chr1:212807800-212811400	Enhancers	Fetal Muscle Leg	muscle
7	chr1:212807800-212812600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:212807800-212812800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:212808000-212810000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:212808000-212812600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:212808200-212809800	Enhancers	Thymus	Thymus
12	chr1:212808200-212810400	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:212808200-212810400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:212808200-212810400	Enhancers	NHLF	lung
15	chr1:212808200-212810600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr1:212808200-212810800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:212808200-212810800	Enhancers	Spleen	Spleen
18	chr1:212808200-212810800	Enhancers	HSMMtube	muscle
19	chr1:212808200-212810800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr1:212808200-212811000	Enhancers	Primary B cells from cord blood	blood
21	chr1:212808200-212811000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:212808200-212812800	Enhancers	Fetal Stomach	stomach
23	chr1:212808200-212813000	Enhancers	Fetal Heart	heart
24	chr1:212808200-212813000	Enhancers	Fetal Thymus	thymus
25	chr1:212808400-212809800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:212808400-212810000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:212808400-212810800	Enhancers	Primary T cells from cord blood	blood
28	chr1:212808400-212810800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:212808400-212810800	Enhancers	Fetal Intestine Small	intestine
30	chr1:212808400-212810800	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:212808400-212810800	Enhancers	Small Intestine	intestine
32	chr1:212808400-212811000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:212808400-212811000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:212808400-212811000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:212808400-212811200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:212808400-212812600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:212808600-212809800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:212808600-212809800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:212808600-212810400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:212808600-212810600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:212808600-212810800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:212808600-212810800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:212808600-212810800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:212808600-212810800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:212808600-212810800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:212808600-212811000	Enhancers	Primary T cells fromperipheralblood	blood
47	chr1:212808600-212811000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:212808600-212811400	Enhancers	NH-A	brain
49	chr1:212808600-212813000	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:212808800-212809800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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