Variant report

Variant	rs12540029
Chromosome Location	chr7:108135579-108135580
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108127744..108131124-chr7:108135356..108137737,3	K562	blood:
2	chr7:108094702..108096715-chr7:108133980..108136057,2	MCF-7	breast:
3	chr7:108126953..108129435-chr7:108135410..108136937,2	K562	blood:
4	chr7:108135257..108139120-chr7:108208944..108212373,4	K562	blood:

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10953572	0.80[EUR][1000 genomes]
rs10953573	0.80[EUR][1000 genomes]
rs11971386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11977071	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11983802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983842	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530879	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536929	0.80[EUR][1000 genomes]
rs12538539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705474	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13224588	0.81[ASN][1000 genomes]
rs13239792	0.90[ASN][1000 genomes]
rs16872576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17134769	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34164886	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34459886	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34771129	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34827770	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34915298	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34959248	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35220845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35444439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35687881	0.80[EUR][1000 genomes]
rs3752639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3763463	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60117684	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6964631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71568523	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71568524	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71568525	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71568529	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71568531	0.82[ASN][1000 genomes]
rs71568533	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7786180	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641410	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641411	0.90[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540029	NRCAM	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:108102400-108137000	Weak transcription	NH-A	brain
3	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
5	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:108106200-108150800	Weak transcription	NHLF	lung
7	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
8	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
12	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
13	chr7:108111000-108137800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:108111400-108142200	Strong transcription	Liver	Liver
15	chr7:108111400-108154800	Weak transcription	NHEK	skin
16	chr7:108111600-108138400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:108111600-108142600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:108111800-108143600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:108113200-108157000	Weak transcription	Psoas Muscle	Psoas
20	chr7:108113600-108140000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:108113800-108150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:108113800-108165800	Weak transcription	Gastric	stomach
23	chr7:108114000-108139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
25	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:108115200-108151800	Weak transcription	NHDF-Ad	bronchial
27	chr7:108116400-108141400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr7:108117200-108150600	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:108117200-108151800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:108119200-108157600	Weak transcription	Brain Germinal Matrix	brain
32	chr7:108119600-108136800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:108119600-108137000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:108119800-108137600	Weak transcription	Brain Anterior Caudate	brain
35	chr7:108119800-108139800	Weak transcription	Brain Angular Gyrus	brain
36	chr7:108119800-108139800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:108119800-108140000	Weak transcription	Fetal Muscle Leg	muscle
38	chr7:108119800-108140200	Weak transcription	Brain Substantia Nigra	brain
39	chr7:108119800-108140600	Weak transcription	Lung	lung
40	chr7:108119800-108140600	Weak transcription	Ovary	ovary
41	chr7:108119800-108144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:108119800-108144200	Weak transcription	Small Intestine	intestine
43	chr7:108119800-108151000	Weak transcription	Fetal Kidney	kidney
44	chr7:108119800-108151800	Weak transcription	Thymus	Thymus
45	chr7:108119800-108151800	Weak transcription	HMEC	breast
46	chr7:108119800-108154800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:108119800-108158200	Weak transcription	Aorta	Aorta
48	chr7:108121600-108158200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:108122000-108141200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:108122000-108144200	Weak transcription	Fetal Brain Male	brain

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