Variant report

Variant	rs203884
Chromosome Location	chr6:28077374-28077375
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27775941..27778895-chr6:28077283..28079265,2	K562	blood:
2	chr6:28057160..28060114-chr6:28076848..28078710,3	K562	blood:
3	chr6:27858238..27861004-chr6:28077246..28078908,2	K562	blood:
4	chr6:28072263..28073986-chr6:28075857..28078538,2	MCF-7	breast:
5	chr6:28074765..28079544-chr6:28088308..28092763,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219891	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1071893	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150666	1.00[ASW][hapmap];0.95[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];0.99[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150678	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12173797	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1225592	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225595	0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225716	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233691	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1233708	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149897	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs149900	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs149942	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs149944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs149945	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs149955	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149958	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149959	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149961	0.90[YRI][hapmap]
rs149962	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149965	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149969	0.89[YRI][hapmap]
rs149970	0.82[CHB][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs149972	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs149989	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs156738	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs156739	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1631552	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172166	0.89[YRI][hapmap]
rs1770131	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17711801	0.86[CEU][hapmap]
rs183244	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203883	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203890	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs203892	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203893	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791332	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713144	0.81[CEU][hapmap]
rs476167	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs536704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755442	0.81[CEU][hapmap]
rs9295759	0.82[CEU][hapmap]
rs9295760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393881	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs9461443	0.86[CEU][hapmap]
rs9468274	0.87[ASW][hapmap];0.90[YRI][hapmap]

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	nsv349384	chr6:28075886-28080766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs203884	OR2B6	cis	parietal	SCAN
rs203884	ZNF187	cis	cerebellum	SCAN
rs203884	ZNF323	cis	Temporal Cortex	GTEx
rs203884	OR2B8P	cis	Thyroid	GTEx
rs203884	ZSCAN31	cis	Thyroid	GTEx
rs203884	ZNF389	cis	lymphoblastoid	seeQTL
rs203884	ZNF323	cis	multi-tissue	Pritchard
rs203884	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs203884	ZNF323	cis	Frontal Cortex	GTEx
rs203884	AL022393.7	cis	Nerve Tibial	GTEx
rs203884	ZSCAN23	cis	cerebellum	SCAN
rs203884	ZNF323	cis	Brain Pons	GTEx
rs203884	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs203884	BTN3A2	cis	multi-tissue	Pritchard
rs203884	ZNF192	cis	cerebellum	SCAN
rs203884	OR1F12	cis	Thyroid	GTEx
rs203884	ZNF323	cis	brain	seeQTL
rs203884	ZNF204P	cis	parietal	SCAN
rs203884	ZNF323	cis	parietal	SCAN
rs203884	ZNF323	cis	Cerebellum	GTEx
rs203884	NKAPL	cis	parietal	SCAN
rs203884	AL022393.7	cis	Artery Tibial	GTEx
rs203884	ZNF187	cis	parietal	SCAN
rs203884	ZNF165	cis	lymphoblastoid	seeQTL
rs203884	ZNF323	cis	cerebellum	SCAN
rs203884	AL022393.7	cis	Heart Left Ventricle	GTEx
rs203884	ZNF192	cis	parietal	SCAN
rs203884	AL022393.7	cis	Muscle Skeletal	GTEx
rs203884	ZKSCAN3	cis	parietal	SCAN
rs203884	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28073000-28083800	Weak transcription	Aorta	Aorta
2	chr6:28073200-28081600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:28073200-28081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:28073200-28082200	Weak transcription	HSMM	muscle
5	chr6:28073200-28082400	Weak transcription	Fetal Stomach	stomach
6	chr6:28073200-28083000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:28073200-28083400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:28073200-28091400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:28073200-28091800	Weak transcription	Right Ventricle	heart
10	chr6:28073400-28080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:28073400-28081200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:28073400-28081600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:28073400-28081600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:28073400-28081600	Weak transcription	HSMMtube	muscle
15	chr6:28073400-28081600	Weak transcription	NH-A	brain
16	chr6:28073400-28081800	Weak transcription	Primary B cells from cord blood	blood
17	chr6:28073400-28082000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:28073400-28082000	Weak transcription	Fetal Thymus	thymus
19	chr6:28073400-28082200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:28073400-28082200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:28073400-28082200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:28073400-28082200	Weak transcription	GM12878-XiMat	blood
23	chr6:28073400-28082400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28073400-28082400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:28073400-28082400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:28073400-28082400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:28073400-28082600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28073400-28082600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:28073400-28082600	Weak transcription	Placenta	Placenta
30	chr6:28073400-28082800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:28073400-28082800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:28073400-28083000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:28073400-28083000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:28073400-28083000	Weak transcription	Fetal Lung	lung
35	chr6:28073400-28083000	Weak transcription	Thymus	Thymus
36	chr6:28073400-28083000	Weak transcription	Spleen	Spleen
37	chr6:28073400-28083200	Weak transcription	Brain Angular Gyrus	brain
38	chr6:28073400-28083400	Weak transcription	A549	lung
39	chr6:28073400-28083600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:28073400-28083600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:28073400-28083600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:28073400-28083600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:28073400-28083600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:28073400-28083600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:28073400-28083600	Weak transcription	Fetal Kidney	kidney
46	chr6:28073400-28083800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:28073400-28083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28073400-28088000	Weak transcription	NHLF	lung
49	chr6:28073400-28091200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:28073400-28091400	Weak transcription	NHDF-Ad	bronchial

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