Variant report

Variant	rs1556487
Chromosome Location	chr9:103213947-103213948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103213146..103215869-chr9:103217613..103219116,2	K562	blood:
2	chr9:103199462..103202264-chr9:103213712..103215287,2	MCF-7	breast:
3	chr9:103212699..103214565-chr9:103243947..103246407,2	K562	blood:
4	chr9:103109668..103111335-chr9:103213495..103215369,2	K562	blood:
5	chr9:103197970..103201753-chr9:103212860..103216897,4	K562	blood:
6	chr9:103205043..103207863-chr9:103213168..103215461,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10819783	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151598	0.82[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1556487	MURC	cis	cerebellum	SCAN
rs1556487	MURC	cis	parietal	SCAN
rs1556487	GALNT12	cis	cerebellum	SCAN
rs1556487	TMEFF1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
2	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
3	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
7	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:103193000-103214400	Weak transcription	Pancreas	Pancrea
11	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
12	chr9:103200000-103217000	Weak transcription	K562	blood
13	chr9:103201200-103215600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:103201600-103215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:103202000-103215800	Weak transcription	Fetal Thymus	thymus
16	chr9:103202800-103217400	Weak transcription	Right Ventricle	heart
17	chr9:103203800-103215600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:103203800-103217400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:103204000-103214000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:103204000-103216800	Strong transcription	Osteobl	bone
21	chr9:103204200-103214000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:103204600-103221200	Weak transcription	Fetal Kidney	kidney
23	chr9:103205000-103214200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:103205000-103214400	Weak transcription	Gastric	stomach
25	chr9:103205000-103216800	Weak transcription	Fetal Intestine Small	intestine
26	chr9:103206000-103217000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:103206800-103214000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:103206800-103216200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr9:103206800-103217000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:103207000-103214400	Weak transcription	Spleen	Spleen
31	chr9:103207000-103217400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:103207000-103227400	Weak transcription	Brain Anterior Caudate	brain
33	chr9:103207200-103214000	Strong transcription	A549	lung
34	chr9:103207400-103214200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:103207600-103215800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:103207600-103216600	Weak transcription	Hela-S3	cervix
37	chr9:103207800-103215000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:103208400-103217400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:103208600-103214200	Weak transcription	Fetal Heart	heart
40	chr9:103208800-103227200	Weak transcription	Brain Angular Gyrus	brain
41	chr9:103208800-103227800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:103209000-103214200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr9:103209000-103217400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:103209600-103214200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:103209600-103216200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr9:103209600-103217800	Weak transcription	HepG2	liver
47	chr9:103209600-103227400	Weak transcription	Brain Substantia Nigra	brain
48	chr9:103210000-103217200	Strong transcription	NHLF	lung
49	chr9:103210000-103217800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:103210200-103214800	Weak transcription	Brain Hippocampus Middle	brain

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