Variant report

Variant	rs2301955
Chromosome Location	chr22:31018646-31018647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31009106..31011344-chr22:31017330..31018949,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10418	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11703570	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs13054912	0.88[ASN][1000 genomes]
rs13055009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13056378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13057127	0.91[ASN][1000 genomes]
rs1544468	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2003503	0.83[ASN][1000 genomes]
rs2301957	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301958	0.86[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs4340628	0.85[ASN][1000 genomes]
rs4353747	0.91[ASN][1000 genomes]
rs4820882	0.85[ASN][1000 genomes]
rs4820888	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820890	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56132790	0.91[ASN][1000 genomes]
rs5749131	0.81[CHB][hapmap]
rs5749132	0.90[ASN][1000 genomes]
rs5749134	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749135	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749142	0.91[ASN][1000 genomes]
rs5749143	0.91[ASN][1000 genomes]
rs5749145	0.91[ASN][1000 genomes]
rs5749148	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs5753229	0.88[ASN][1000 genomes]
rs5753234	0.91[ASN][1000 genomes]
rs5753246	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753247	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753249	0.86[ASN][1000 genomes]
rs5753257	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs5753260	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5997703	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997709	0.90[ASN][1000 genomes]
rs5997710	0.90[ASN][1000 genomes]
rs5997727	0.85[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs7286680	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289553	0.91[ASN][1000 genomes]
rs731990	0.91[ASN][1000 genomes]
rs731991	0.91[ASN][1000 genomes]
rs740233	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs740235	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8138932	0.83[ASN][1000 genomes]
rs8630	0.85[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs9609017	0.85[ASN][1000 genomes]
rs9621047	0.81[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3359938	chr22:31018577-31021325	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2301955	PES1	cis	parietal	SCAN
rs2301955	CRYBB3	cis	parietal	SCAN
rs2301955	ZNRF3	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31003200-31031200	Weak transcription	Aorta	Aorta
2	chr22:31003800-31030600	Weak transcription	Thymus	Thymus
3	chr22:31004400-31020200	Weak transcription	Fetal Kidney	kidney
4	chr22:31005000-31022200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr22:31006000-31019200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr22:31006000-31020800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr22:31006000-31023200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:31006000-31023200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:31006000-31030400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr22:31006000-31030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:31006000-31030600	Weak transcription	Colonic Mucosa	Colon
12	chr22:31006200-31019400	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr22:31006200-31023800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr22:31006200-31030600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:31006400-31023000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr22:31006400-31023200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:31006400-31023400	Strong transcription	Fetal Intestine Small	intestine
18	chr22:31006600-31020000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr22:31006600-31030400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:31006800-31030200	Weak transcription	Placenta	Placenta
21	chr22:31007000-31030600	Weak transcription	Fetal Brain Male	brain
22	chr22:31007200-31019200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:31007600-31030200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:31008000-31030400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr22:31008400-31023200	Strong transcription	Adipose Nuclei	Adipose
26	chr22:31008800-31019000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:31010200-31022400	Weak transcription	HUVEC	blood vessel
28	chr22:31011200-31019600	Strong transcription	Fetal Muscle Leg	muscle
29	chr22:31011600-31024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:31011600-31026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr22:31011800-31019200	Strong transcription	Spleen	Spleen
32	chr22:31011800-31030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr22:31011800-31030600	Weak transcription	Right Ventricle	heart
34	chr22:31012000-31023800	Weak transcription	Brain Anterior Caudate	brain
35	chr22:31012000-31030600	Weak transcription	Brain Angular Gyrus	brain
36	chr22:31012200-31024600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:31013000-31023200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:31013600-31030600	Weak transcription	Pancreas	Pancrea
39	chr22:31013800-31022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr22:31013800-31022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:31013800-31030600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr22:31014000-31030200	Weak transcription	Brain Substantia Nigra	brain
43	chr22:31014000-31030400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr22:31014000-31030800	Weak transcription	Gastric	stomach
45	chr22:31014000-31030800	Weak transcription	Ovary	ovary
46	chr22:31015000-31024200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:31015200-31020800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr22:31015800-31030600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:31015800-31030600	Weak transcription	Fetal Lung	lung
50	chr22:31016000-31022000	Weak transcription	Fetal Intestine Large	intestine

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