Variant report

Variant	rs322840
Chromosome Location	chr7:127708975-127708976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127707231..127709152-chr7:127855482..127857395,2	K562	blood:
2	chr7:127681336..127683233-chr7:127708637..127710804,2	MCF-7	breast:
3	chr7:127707718..127710991-chr7:127715839..127718158,3	K562	blood:
4	chr7:127707623..127710544-chr7:127711576..127714237,2	K562	blood:
5	chr7:127703319..127705715-chr7:127706907..127711079,5	K562	blood:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1024910	0.87[AMR][1000 genomes]
rs1193333	0.83[AMR][1000 genomes]
rs1193335	0.84[AMR][1000 genomes]
rs124756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345509	0.83[JPT][hapmap]
rs2241291	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs2543477	0.82[AMR][1000 genomes]
rs322781	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs322813	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs322816	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322817	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs322819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs322820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322822	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322823	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322824	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs322825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322826	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs322827	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322828	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322829	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322830	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322832	0.99[ASN][1000 genomes]
rs322833	0.99[ASN][1000 genomes]
rs322837	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757753	0.98[ASN][1000 genomes]
rs3757754	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757759	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757760	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs3757763	0.85[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes]
rs3757771	0.81[AMR][1000 genomes]
rs3779522	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779526	0.83[JPT][hapmap]
rs3779527	0.90[AMR][1000 genomes]
rs3808055	0.98[ASN][1000 genomes]
rs3808056	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs3808088	0.81[CHB][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap]
rs3823995	0.83[JPT][hapmap]
rs6467155	0.88[AMR][1000 genomes]
rs6467156	0.88[AMR][1000 genomes]
rs6969233	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6973092	0.83[JPT][hapmap]
rs7789322	0.89[AMR][1000 genomes]

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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs322840	CCDC136	cis	parietal	SCAN
rs322840	TCN2	trans	lymphoblastoid	seeQTL
rs322840	GPR37	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
2	chr7:127669600-127718200	Weak transcription	A549	lung
3	chr7:127673200-127712000	Weak transcription	Esophagus	oesophagus
4	chr7:127673800-127715400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:127681000-127716200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:127681200-127718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:127681600-127714600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:127685000-127710400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:127689400-127717000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:127692800-127714400	Weak transcription	Right Ventricle	heart
11	chr7:127692800-127724200	Weak transcription	Right Atrium	heart
12	chr7:127693200-127718400	Weak transcription	HMEC	breast
13	chr7:127693400-127711600	Weak transcription	Adipose Nuclei	Adipose
14	chr7:127693400-127714200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:127693400-127716600	Weak transcription	Colonic Mucosa	Colon
16	chr7:127693400-127717200	Weak transcription	Small Intestine	intestine
17	chr7:127693600-127710200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:127694400-127713600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:127694400-127716800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:127694800-127717200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:127695200-127718000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:127697200-127714800	Weak transcription	HUVEC	blood vessel
23	chr7:127698200-127713600	Weak transcription	Osteobl	bone
24	chr7:127698400-127714600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:127699800-127714600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:127700000-127712000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:127700400-127711600	Weak transcription	Dnd41	blood
28	chr7:127700400-127714600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:127700400-127714600	Weak transcription	Left Ventricle	heart
30	chr7:127700400-127714800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:127700400-127715400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:127700400-127715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr7:127700800-127711800	Weak transcription	Thymus	Thymus
34	chr7:127701000-127712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:127701200-127713000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr7:127701600-127712200	Weak transcription	NHLF	lung
37	chr7:127701600-127724600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:127701800-127714400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:127702000-127711000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr7:127702000-127712800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:127702200-127714800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:127702800-127727800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:127703200-127715600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:127703400-127710000	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:127703400-127715600	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:127703400-127715600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:127703400-127715800	Weak transcription	NH-A	brain
48	chr7:127703600-127709000	Weak transcription	Gastric	stomach
49	chr7:127703600-127709000	Weak transcription	Pancreas	Pancrea
50	chr7:127703600-127712000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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