Variant report

Variant	rs3856637
Chromosome Location	chr3:136391195-136391196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136388635..136392149-chr3:136467930..136472508,4	K562	blood:
2	chr3:136389835..136392302-chr3:136408179..136409824,2	MCF-7	breast:
3	chr3:136389263..136391478-chr3:136467252..136469430,2	K562	blood:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1017881	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1070232	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10935186	0.93[JPT][hapmap]
rs11919030	0.93[JPT][hapmap]
rs12630999	0.86[ASW][hapmap];0.90[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs12635723	0.87[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs13068119	0.80[CEU][hapmap];0.83[MEX][hapmap]
rs1394092	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs1681818	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs1729951	0.87[JPT][hapmap]
rs2062322	0.93[JPT][hapmap]
rs34553037	0.80[CEU][hapmap];0.89[MEX][hapmap]
rs34602896	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs34967300	0.80[CEU][hapmap];0.83[MEX][hapmap]
rs34992220	0.87[CHD][hapmap]
rs4038578	0.93[JPT][hapmap]
rs4408829	0.93[JPT][hapmap]
rs4456810	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4521165	1.00[JPT][hapmap]
rs4678433	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs4678437	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4678438	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6439649	1.00[JPT][hapmap]
rs6791142	0.93[JPT][hapmap]
rs6794351	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs6802702	0.93[JPT][hapmap]
rs6808312	1.00[JPT][hapmap]
rs699165	0.80[ASW][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs711975	0.93[JPT][hapmap]
rs7432375	0.93[JPT][hapmap]
rs7616204	0.93[JPT][hapmap]
rs7618518	1.00[JPT][hapmap]
rs7618871	0.93[JPT][hapmap]
rs7621025	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap]
rs833752	1.00[ASW][hapmap];0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs900048	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs900818	0.93[JPT][hapmap]
rs9289511	0.89[CHB][hapmap]
rs940174	0.93[JPT][hapmap]
rs9820485	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs9833207	0.89[CHB][hapmap];0.87[CHD][hapmap]
rs9836231	0.93[JPT][hapmap]
rs9845762	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9854084	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9883916	0.80[CEU][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3856637	MSL2	cis	cerebellum	SCAN
rs3856637	PCCB	cis	lymphoblastoid	seeQTL
rs3856637	NCK1	cis	parietal	SCAN
rs3856637	PCCB	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136365000-136396400	Weak transcription	Gastric	stomach
2	chr3:136376600-136392200	Weak transcription	Placenta	Placenta
3	chr3:136378600-136391400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:136378600-136393600	Weak transcription	Fetal Lung	lung
5	chr3:136378600-136394000	Weak transcription	Adipose Nuclei	Adipose
6	chr3:136379200-136394000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:136379600-136391800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:136380800-136391600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:136381600-136392400	Weak transcription	Small Intestine	intestine
10	chr3:136381800-136410800	Weak transcription	Psoas Muscle	Psoas
11	chr3:136382600-136394200	Weak transcription	Fetal Heart	heart
12	chr3:136383000-136393200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:136383400-136394800	Weak transcription	Ovary	ovary
14	chr3:136383600-136395800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:136383800-136391400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:136383800-136391800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:136384000-136392400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:136384200-136391400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:136384200-136392000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:136384200-136392000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:136384200-136393200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:136384200-136393800	Weak transcription	Brain Substantia Nigra	brain
23	chr3:136384400-136391400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:136384400-136392000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:136385200-136392000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:136385200-136394000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:136385200-136398400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:136385400-136392400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:136385400-136393800	Weak transcription	Stomach Mucosa	stomach
30	chr3:136385600-136394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:136386200-136393600	Weak transcription	NHLF	lung
32	chr3:136386400-136393800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:136386400-136412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:136386600-136394000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:136387000-136394800	Weak transcription	K562	blood
36	chr3:136387000-136396400	Weak transcription	Esophagus	oesophagus
37	chr3:136387200-136412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:136387600-136393200	Weak transcription	Lung	lung
39	chr3:136387800-136397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:136388000-136393200	Weak transcription	Primary B cells from cord blood	blood
41	chr3:136388000-136393200	Weak transcription	GM12878-XiMat	blood
42	chr3:136388200-136392200	Weak transcription	Fetal Thymus	thymus
43	chr3:136388200-136393600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:136388400-136392000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:136388400-136392200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:136388400-136392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:136389200-136393200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:136389600-136394000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:136389600-136395400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:136390000-136393200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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