Variant report

Variant	rs6828807
Chromosome Location	chr4:7798886-7798887
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	chr4:7787308..7789396-chr4:7796554..7799014,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10015031	0.86[ASN][1000 genomes]
rs10025154	0.86[ASN][1000 genomes]
rs10029941	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs10032821	0.80[ASN][1000 genomes]
rs12645231	0.82[ASN][1000 genomes]
rs13109291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13136890	0.87[YRI][hapmap]
rs1557817	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16841211	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16841229	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2018399	0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap]
rs2107182	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs28460880	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28475763	0.89[AFR][1000 genomes]
rs28729246	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4234829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4388087	0.85[CHB][hapmap]
rs4404542	0.85[CHB][hapmap]
rs4413405	0.85[CHB][hapmap]
rs55689818	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60422709	0.83[EUR][1000 genomes]
rs60840998	0.88[EUR][1000 genomes]
rs6446619	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827395	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6829473	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838291	0.82[CHB][hapmap]
rs6852990	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs756255	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9917925	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6828807	CRMP1	cis	parietal	SCAN
rs6828807	CRMP1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
12	chr4:7783400-7799200	Weak transcription	HepG2	liver
13	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
16	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
18	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
19	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:7786000-7800800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:7787200-7799000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:7787400-7800200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:7789400-7799000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:7790800-7800800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:7790800-7803600	Strong transcription	HSMM	muscle
30	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
32	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:7791200-7800800	Weak transcription	Spleen	Spleen
34	chr4:7791400-7800400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:7791600-7799000	Weak transcription	Gastric	stomach
37	chr4:7791600-7799000	Weak transcription	Pancreas	Pancrea
38	chr4:7791600-7800000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:7791600-7800400	Weak transcription	Left Ventricle	heart
40	chr4:7791600-7800400	Weak transcription	Right Ventricle	heart
41	chr4:7791600-7801200	Weak transcription	Fetal Brain Male	brain
42	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:7792600-7803400	Strong transcription	A549	lung
45	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
46	chr4:7793200-7799200	Weak transcription	Primary T cells from cord blood	blood
47	chr4:7793200-7803800	Strong transcription	NH-A	brain
48	chr4:7794200-7799200	Weak transcription	Lung	lung
49	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:7794600-7799000	Weak transcription	Rectal Smooth Muscle	rectum

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