Variant report

Variant	rs131296
Chromosome Location	chr22:30174229-30174230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30171892..30174672-chr22:30194273..30195862,2	K562	blood:
2	chr22:30161672..30165971-chr22:30171694..30174809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction
ENSG00000184076	Chromatin interaction
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1076137	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12168552	0.83[AMR][1000 genomes]
rs131278	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs131291	0.87[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs131294	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140105	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs140108	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs140125	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140135	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs140142	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs140151	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17643918	0.83[AMR][1000 genomes]
rs2105870	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2349225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412960	0.87[CEU][hapmap]
rs249400	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34862234	0.83[AMR][1000 genomes]
rs35705048	0.83[AMR][1000 genomes]
rs36578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36600	0.87[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs36604	0.87[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs3887275	0.87[CEU][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs3958025	0.87[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[YRI][hapmap]
rs4239932	0.87[CEU][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap]
rs4820820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4823055	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4823063	0.87[CEU][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs5752968	0.95[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7286070	0.80[AMR][1000 genomes]
rs7292615	0.83[AMR][1000 genomes]
rs8139994	0.82[AMR][1000 genomes]
rs8141680	0.89[YRI][hapmap]
rs9620926	0.83[AMR][1000 genomes]
rs9625874	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv989381	chr22:30170518-30177035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs131296	NEFH	cis	cerebellum	SCAN
rs131296	TTC28	cis	cerebellum	SCAN
rs131296	CRYBB3	cis	parietal	SCAN
rs131296	KIAA1671	cis	cerebellum	SCAN
rs131296	UCRC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr22:30165400-30176800	Weak transcription	Fetal Brain Male	brain
5	chr22:30166000-30176800	Weak transcription	Fetal Kidney	kidney
6	chr22:30166400-30176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:30166600-30176800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30166600-30177000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr22:30166600-30183800	Weak transcription	Aorta	Aorta
10	chr22:30166800-30176400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30166800-30176400	Weak transcription	Colon Smooth Muscle	Colon
12	chr22:30166800-30176400	Weak transcription	Small Intestine	intestine
13	chr22:30166800-30176800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr22:30166800-30176800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr22:30166800-30182800	Weak transcription	Primary T cells from cord blood	blood
16	chr22:30166800-30183000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr22:30166800-30183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr22:30166800-30183800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr22:30166800-30184200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:30167000-30174800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:30167000-30175000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr22:30167000-30176400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr22:30167000-30176400	Weak transcription	Brain Angular Gyrus	brain
25	chr22:30167000-30176400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:30167000-30176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr22:30167000-30176800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:30167000-30176800	Weak transcription	Brain Germinal Matrix	brain
29	chr22:30167000-30180400	Weak transcription	Fetal Brain Female	brain
30	chr22:30167000-30183400	Weak transcription	Primary B cells from cord blood	blood
31	chr22:30167000-30183600	Weak transcription	Dnd41	blood
32	chr22:30167200-30174800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:30167200-30175000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr22:30167200-30175000	Weak transcription	Spleen	Spleen
35	chr22:30167200-30176600	Weak transcription	Brain Hippocampus Middle	brain
36	chr22:30167200-30176600	Weak transcription	Brain Substantia Nigra	brain
37	chr22:30167200-30176600	Weak transcription	Ovary	ovary
38	chr22:30167200-30176800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr22:30167200-30177200	Weak transcription	Lung	lung
40	chr22:30167200-30183000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr22:30167200-30183200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr22:30167200-30183200	Weak transcription	GM12878-XiMat	blood
43	chr22:30167200-30184000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr22:30167200-30184000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr22:30167200-30187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr22:30167400-30175400	Weak transcription	Left Ventricle	heart
47	chr22:30167400-30175600	Weak transcription	Psoas Muscle	Psoas
48	chr22:30167400-30175800	Weak transcription	Right Ventricle	heart
49	chr22:30167400-30176400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr22:30167400-30176400	Weak transcription	Esophagus	oesophagus

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