Variant report

Variant	rs3923394
Chromosome Location	chr1:151748425-151748426
allele	G/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151747348..151750868-chr1:151751909..151754177,3	MCF-7	breast:
2	chr1:151747278..151749965-chr1:151750344..151752531,2	K562	blood:
3	chr1:151747330..151748912-chr1:151773783..151775986,2	MCF-7	breast:
4	chr1:151747841..151749878-chr1:151812663..151815649,2	MCF-7	breast:
5	chr1:151747278..151749965-chr1:151750344..151752531,3	K562	blood:
6	chr1:151747349..151749226-chr1:151752622..151754895,2	K562	blood:
7	chr1:151747349..151750061-chr1:151752622..151754355,2	K562	blood:
8	chr1:151747872..151750069-chr1:151755565..151757343,2	K562	blood:
9	chr1:151747136..151750558-chr1:151761891..151764421,4	K562	blood:
10	chr1:151741435..151743883-chr1:151746073..151749758,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225556	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000182134	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1054475	0.81[GIH][hapmap]
rs10888435	0.83[CEU][hapmap];0.94[EUR][1000 genomes]
rs11204887	0.95[EUR][1000 genomes]
rs11204888	0.95[EUR][1000 genomes]
rs1123855	0.81[GIH][hapmap]
rs12066445	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs12073999	0.96[EUR][1000 genomes]
rs12409493	0.84[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs12567867	0.92[EUR][1000 genomes]
rs1781419	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs1781421	0.81[GIH][hapmap]
rs1781423	0.81[GIH][hapmap]
rs2293088	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs33911740	0.94[EUR][1000 genomes]
rs3748612	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4845572	0.95[EUR][1000 genomes]
rs6667279	0.98[EUR][1000 genomes]
rs6679233	0.96[CEU][hapmap];1.00[TSI][hapmap]
rs7534811	0.84[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs868868	0.84[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs9017	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826	0.84[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3923394	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs3923394	S100A13	cis	cerebellum	SCAN
rs3923394	BCL9	cis	cerebellum	SCAN
rs3923394	LCE1C	cis	parietal	SCAN
rs3923394	LINGO4	cis	cerebellum	SCAN
rs3923394	TDRKH	cis	cerebellum	SCAN
rs3923394	TDRKH	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736600-151751000	Weak transcription	Ovary	ovary
2	chr1:151736800-151750800	Weak transcription	Right Atrium	heart
3	chr1:151736800-151762600	Weak transcription	Gastric	stomach
4	chr1:151737000-151752200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:151737000-151762400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:151737000-151762400	Weak transcription	HSMMtube	muscle
7	chr1:151737000-151762600	Weak transcription	Small Intestine	intestine
8	chr1:151737200-151753800	Weak transcription	A549	lung
9	chr1:151738600-151750600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:151739400-151753200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:151740800-151759000	Weak transcription	Esophagus	oesophagus
12	chr1:151741000-151762600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:151741200-151753000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:151741200-151756200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:151742400-151755200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:151742800-151762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:151744000-151762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:151744200-151750600	Weak transcription	Fetal Intestine Large	intestine
19	chr1:151744600-151762200	Weak transcription	Primary B cells from cord blood	blood
20	chr1:151745200-151752600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:151745200-151752800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151745400-151749800	Strong transcription	Fetal Brain Female	brain
23	chr1:151745400-151753200	Weak transcription	Fetal Kidney	kidney
24	chr1:151745400-151755600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:151745600-151754400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:151745600-151755400	Strong transcription	Primary T cells from cord blood	blood
27	chr1:151745800-151749400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:151745800-151752800	Strong transcription	Brain Substantia Nigra	brain
29	chr1:151745800-151754600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:151745800-151754600	Strong transcription	Brain Germinal Matrix	brain
31	chr1:151745800-151755000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:151745800-151755400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:151745800-151755600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:151745800-151755600	Strong transcription	Dnd41	blood
35	chr1:151746000-151749200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:151746000-151752800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:151746000-151754600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:151746000-151762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:151746200-151748600	Strong transcription	Placenta	Placenta
40	chr1:151746200-151748800	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr1:151746200-151749600	Strong transcription	Lung	lung
42	chr1:151746200-151751800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:151746200-151752000	Strong transcription	Fetal Thymus	thymus
44	chr1:151746200-151752000	Strong transcription	Thymus	Thymus
45	chr1:151746200-151752400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:151746200-151752600	Strong transcription	Adipose Nuclei	Adipose
47	chr1:151746200-151752600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:151746200-151752800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:151746200-151753000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:151746200-151754600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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