Variant report

Variant	rs131291
Chromosome Location	chr22:30169436-30169437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30168312..30170013-chr22:30216889..30218868,2	MCF-7	breast:
2	chr22:30168082..30170314-chr22:30185958..30187695,2	MCF-7	breast:
3	chr22:30167944..30169824-chr22:30191784..30194571,2	MCF-7	breast:
4	chr22:30161450..30165931-chr22:30167852..30170164,6	K562	blood:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction
ENSG00000184076	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1076137	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs131278	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs131294	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs131296	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]
rs140105	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs140108	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs140125	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs140135	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140142	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140151	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2349225	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs249400	0.85[ASN][1000 genomes]
rs36578	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36600	0.82[ASW][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs36604	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap]
rs3887275	0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs3958025	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4239932	0.84[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs4820820	0.80[AMR][1000 genomes]
rs4823055	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4823063	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap]
rs5752968	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8141680	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv817987	chr22:30163526-30169436	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs131291	KIAA1671	cis	cerebellum	SCAN
rs131291	CRYBB3	cis	parietal	SCAN
rs131291	UCRC	Cis_1M	lymphoblastoid	RTeQTL
rs131291	TTC28	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30171000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr22:30165000-30172400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr22:30165400-30176800	Weak transcription	Fetal Brain Male	brain
7	chr22:30166000-30169800	Enhancers	HepG2	liver
8	chr22:30166000-30176800	Weak transcription	Fetal Kidney	kidney
9	chr22:30166400-30176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:30166600-30176800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:30166600-30177000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr22:30166600-30183800	Weak transcription	Aorta	Aorta
13	chr22:30166800-30172600	Weak transcription	K562	blood
14	chr22:30166800-30174200	Weak transcription	Pancreas	Pancrea
15	chr22:30166800-30176400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:30166800-30176400	Weak transcription	Colon Smooth Muscle	Colon
17	chr22:30166800-30176400	Weak transcription	Small Intestine	intestine
18	chr22:30166800-30176800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr22:30166800-30176800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:30166800-30182800	Weak transcription	Primary T cells from cord blood	blood
21	chr22:30166800-30183000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr22:30166800-30183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr22:30166800-30183800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr22:30166800-30184200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr22:30167000-30174800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr22:30167000-30175000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr22:30167000-30176400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:30167000-30176400	Weak transcription	Brain Angular Gyrus	brain
30	chr22:30167000-30176400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr22:30167000-30176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:30167000-30176800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr22:30167000-30176800	Weak transcription	Brain Germinal Matrix	brain
34	chr22:30167000-30180400	Weak transcription	Fetal Brain Female	brain
35	chr22:30167000-30183400	Weak transcription	Primary B cells from cord blood	blood
36	chr22:30167000-30183600	Weak transcription	Dnd41	blood
37	chr22:30167200-30173800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:30167200-30174200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr22:30167200-30174800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:30167200-30175000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr22:30167200-30175000	Weak transcription	Spleen	Spleen
42	chr22:30167200-30176600	Weak transcription	Brain Hippocampus Middle	brain
43	chr22:30167200-30176600	Weak transcription	Brain Substantia Nigra	brain
44	chr22:30167200-30176600	Weak transcription	Ovary	ovary
45	chr22:30167200-30176800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr22:30167200-30177200	Weak transcription	Lung	lung
47	chr22:30167200-30183000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr22:30167200-30183200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr22:30167200-30183200	Weak transcription	GM12878-XiMat	blood
50	chr22:30167200-30184000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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