Variant report

Variant	rs31929
Chromosome Location	chr5:14678369-14678370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:14678101-14678565	GM12878	blood:	n/a	n/a
2	ZNF143	chr5:14678201-14678437	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:14677950-14678726	GM12878	blood:	n/a	n/a
4	RUNX3	chr5:14678336-14679612	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14448785..14450697-chr5:14676194..14678624,2	MCF-7	breast:
2	chr5:14663431..14670152-chr5:14672054..14680588,17	K562	blood:

Variant related genes	Relation type
FAM105B	TF binding region
ENSG00000261360	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs13189930	0.87[JPT][hapmap]
rs149181	0.82[ASN][1000 genomes]
rs149493	0.84[ASN][1000 genomes]
rs149617	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs152788	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs153829	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs153830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs166127	0.88[ASN][1000 genomes]
rs183681	0.91[ASN][1000 genomes]
rs1875513	1.00[JPT][hapmap]
rs2455402	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs250435	0.93[ASN][1000 genomes]
rs250438	0.92[YRI][hapmap]
rs250439	0.84[ASN][1000 genomes]
rs250440	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs250862	0.86[ASN][1000 genomes]
rs251496	0.87[ASN][1000 genomes]
rs258290	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs258374	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs25945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs25951	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs25952	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs25983	0.87[JPT][hapmap]
rs25986	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs25987	0.91[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs25988	0.91[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs25992	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs26307	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs27356	0.87[JPT][hapmap]
rs27882	1.00[ASN][1000 genomes]
rs27911	0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs28004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs31919	0.99[ASN][1000 genomes]
rs31920	0.90[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs31921	0.98[ASN][1000 genomes]
rs31922	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs31923	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs31924	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs31925	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs31926	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs31928	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs31930	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs31968	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs3866215	0.85[JPT][hapmap]
rs40578	0.99[ASN][1000 genomes]
rs42358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs42410	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs456180	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs459467	0.87[ASN][1000 genomes]
rs466880	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4702043	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6554856	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6872954	1.00[JPT][hapmap]
rs6892588	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs745328	0.93[JPT][hapmap]
rs95492	0.81[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1801565	chr5:14671030-14684471	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs31929	FAM105B	Cis_1M	lymphoblastoid	RTeQTL
rs31929	DNAH5	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14666400-14681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:14666400-14688200	Weak transcription	Ovary	ovary
3	chr5:14666600-14688200	Weak transcription	Brain Germinal Matrix	brain
4	chr5:14667000-14680000	Weak transcription	Fetal Brain Female	brain
5	chr5:14667000-14681200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:14667000-14690400	Weak transcription	Fetal Brain Male	brain
7	chr5:14672000-14684200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:14672200-14690400	Strong transcription	Hela-S3	cervix
9	chr5:14672600-14678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:14672800-14679200	Weak transcription	HUVEC	blood vessel
11	chr5:14673000-14679200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:14673000-14679200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:14673000-14681400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:14673200-14681400	Weak transcription	Brain Angular Gyrus	brain
15	chr5:14673800-14679000	Weak transcription	A549	lung
16	chr5:14673800-14690000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
18	chr5:14674200-14679200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:14674600-14679200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:14674600-14681400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:14674600-14687200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:14674600-14688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:14674600-14695600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:14675200-14695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:14675600-14682200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:14675800-14679200	Weak transcription	Brain Anterior Caudate	brain
27	chr5:14675800-14679200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:14675800-14680600	Enhancers	Fetal Heart	heart
29	chr5:14675800-14685400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:14676000-14678800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:14676000-14682000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:14676200-14679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:14676200-14681600	Weak transcription	Brain Substantia Nigra	brain
34	chr5:14676400-14678600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:14676600-14678600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:14676600-14679200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:14676600-14681400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:14676800-14678400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:14676800-14679000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:14676800-14679200	Weak transcription	Esophagus	oesophagus
41	chr5:14676800-14679200	Weak transcription	Gastric	stomach
42	chr5:14676800-14679200	Weak transcription	Pancreas	Pancrea
43	chr5:14676800-14679200	Weak transcription	Thymus	Thymus
44	chr5:14676800-14679400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr5:14676800-14680400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:14676800-14680600	Weak transcription	Colonic Mucosa	Colon
47	chr5:14676800-14681200	Weak transcription	Fetal Lung	lung
48	chr5:14676800-14681400	Weak transcription	Small Intestine	intestine
49	chr5:14676800-14683600	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:14676800-14687800	Weak transcription	Fetal Kidney	kidney

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