Variant report

Variant	rs6587522
Chromosome Location	chr1:150779755-150779756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150779741-150780230	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:150779715-150780227	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:150779601-150780253	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150779291..150781180-chr1:150784227..150787241,3	K562	blood:
2	chr1:150668066..150670376-chr1:150778150..150781017,2	K562	blood:
3	chr1:150668010..150669720-chr1:150777076..150779971,2	MCF-7	breast:
4	chr1:150668066..150670256-chr1:150778150..150780706,2	K562	blood:

Variant related genes	Relation type
CTSK	TF binding region
ENSG00000200175	Chromatin interaction
ENSG00000143457	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10788796	1.00[CEU][hapmap]
rs11204728	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1241576	1.00[CEU][hapmap]
rs1415146	1.00[CEU][hapmap]
rs1415147	1.00[AMR][1000 genomes]
rs267727	1.00[CEU][hapmap]
rs267728	1.00[CEU][hapmap]
rs6587519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6587521	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6587534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6688430	1.00[CEU][hapmap]
rs7515228	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7517945	1.00[AMR][1000 genomes]
rs7518440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518546	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7533914	1.00[CEU][hapmap]
rs7536645	1.00[CEU][hapmap]

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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150761200-150783200	Weak transcription	GM12878-XiMat	blood
2	chr1:150762400-150780000	Weak transcription	NHEK	skin
3	chr1:150764600-150781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:150765400-150781400	Weak transcription	HMEC	breast
5	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
6	chr1:150767600-150783600	Weak transcription	Psoas Muscle	Psoas
7	chr1:150767800-150780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:150768200-150784000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:150769400-150785200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:150770000-150781600	Weak transcription	HSMMtube	muscle
11	chr1:150770400-150783400	Weak transcription	Stomach Mucosa	stomach
12	chr1:150770600-150783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:150770800-150780600	Weak transcription	Esophagus	oesophagus
14	chr1:150771200-150784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:150771200-150785400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:150771400-150783000	Weak transcription	Brain Germinal Matrix	brain
17	chr1:150771600-150785200	Weak transcription	Pancreas	Pancrea
18	chr1:150771800-150783600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:150771800-150783600	Weak transcription	A549	lung
20	chr1:150772000-150780600	Weak transcription	Fetal Brain Female	brain
21	chr1:150772200-150779800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:150772200-150779800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:150772200-150779800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:150772200-150779800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:150772200-150779800	Weak transcription	Fetal Intestine Large	intestine
26	chr1:150772200-150780000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:150772200-150780000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:150772200-150780200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:150772200-150780200	Weak transcription	Brain Substantia Nigra	brain
30	chr1:150772200-150780600	Weak transcription	Left Ventricle	heart
31	chr1:150772200-150780800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:150772200-150782200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:150772200-150782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:150772200-150782400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:150772200-150782400	Weak transcription	Lung	lung
36	chr1:150772200-150783200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:150772200-150783200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:150772200-150783200	Weak transcription	Spleen	Spleen
39	chr1:150772400-150779800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:150772400-150782800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:150772400-150783600	Weak transcription	Right Ventricle	heart
42	chr1:150772600-150779800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:150772600-150780000	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:150772600-150785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:150773000-150783400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:150773200-150782200	Weak transcription	NH-A	brain
47	chr1:150773400-150780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:150773600-150779800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:150773600-150782200	Weak transcription	HSMM	muscle
50	chr1:150775800-150784600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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