Variant report

Variant	rs6005967
Chromosome Location	chr22:29446975-29446976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29446612..29448382-chr22:29463613..29465262,2	MCF-7	breast:
2	chr22:29445328..29447248-chr22:29662863..29665111,2	K562	blood:
3	chr22:29444650..29447110-chr22:29467115..29469245,2	K562	blood:
4	chr22:29445976..29447498-chr22:29467768..29470564,2	MCF-7	breast:
5	chr22:29433370..29436929-chr22:29445281..29448151,3	K562	blood:
6	chr22:29444708..29447348-chr22:29547700..29550186,2	K562	blood:

Variant related genes	Relation type
ENSG00000100263	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000183762	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11704898	0.81[AMR][1000 genomes]
rs12484832	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12485244	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17440734	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs1977047	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1983553	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs2064084	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs2103544	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347789	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2347790	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28541979	0.89[EUR][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs4333023	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4404379	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4594553	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4616575	0.92[ASN][1000 genomes]
rs469994	0.96[CEU][hapmap]
rs4820794	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4823002	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[TSI][hapmap]
rs4823003	0.93[CEU][hapmap]
rs4823005	0.93[CEU][hapmap]
rs5997430	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997431	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997433	0.93[CEU][hapmap]
rs5997434	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5997435	0.90[EUR][1000 genomes]
rs6005955	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005956	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005958	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6005959	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005964	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005965	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs713834	1.00[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs727892	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7284304	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287517	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7290304	0.93[CEU][hapmap]
rs738246	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8137254	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8137499	0.96[CEU][hapmap]
rs8142591	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874915	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs874916	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608719	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9608721	0.87[EUR][1000 genomes]
rs9613768	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs9613771	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613776	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613777	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613782	0.84[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9613784	0.88[EUR][1000 genomes]
rs9613785	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs964589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6005967	SEZ6L	cis	cerebellum	SCAN
rs6005967	GGT5	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
3	chr22:29437200-29450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:29437800-29448800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:29437800-29450200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:29438000-29447200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr22:29438200-29447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:29438400-29449800	Strong transcription	Fetal Stomach	stomach
9	chr22:29438400-29451800	Strong transcription	Fetal Intestine Small	intestine
10	chr22:29439000-29447400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr22:29439000-29447400	Strong transcription	Fetal Intestine Large	intestine
12	chr22:29439000-29447400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr22:29439000-29449800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr22:29439000-29450200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:29439200-29447000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:29439200-29447400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr22:29439200-29447400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr22:29439200-29447400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr22:29439200-29447400	Strong transcription	Pancreas	Pancrea
20	chr22:29439200-29447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr22:29439200-29447600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:29439400-29447000	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr22:29439400-29447400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr22:29439400-29448400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr22:29439400-29448400	Strong transcription	Brain Anterior Caudate	brain
26	chr22:29440000-29447400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr22:29440000-29447400	Strong transcription	Spleen	Spleen
28	chr22:29440000-29447600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr22:29440000-29451400	Weak transcription	Fetal Thymus	thymus
30	chr22:29440200-29448800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr22:29440400-29447000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr22:29440400-29447400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:29440400-29447400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:29440600-29447400	Strong transcription	Lung	lung
35	chr22:29440800-29447400	Strong transcription	Adipose Nuclei	Adipose
36	chr22:29440800-29447400	Strong transcription	Colon Smooth Muscle	Colon
37	chr22:29440800-29448000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr22:29441000-29447400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr22:29441000-29449200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:29441000-29451200	Weak transcription	HSMM	muscle
41	chr22:29441000-29457000	Weak transcription	HUVEC	blood vessel
42	chr22:29441200-29447400	Strong transcription	Liver	Liver
43	chr22:29441200-29447400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:29441200-29447400	Strong transcription	HepG2	liver
45	chr22:29441200-29449600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr22:29441200-29458000	Weak transcription	HMEC	breast
47	chr22:29441400-29447200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr22:29441600-29447400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr22:29441800-29447200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr22:29442000-29447400	Strong transcription	Brain Hippocampus Middle	brain

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