Variant report

Variant	rs3130364
Chromosome Location	chr6:30319154-30319155
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11158	0.81[EUR][1000 genomes]
rs1573296	0.80[EUR][1000 genomes]
rs1970	0.80[EUR][1000 genomes]
rs2106072	0.81[EUR][1000 genomes]
rs2157678	0.80[EUR][1000 genomes]
rs2517609	0.88[EUR][1000 genomes]
rs2517617	0.88[EUR][1000 genomes]
rs2517622	0.81[EUR][1000 genomes]
rs2523712	0.88[EUR][1000 genomes]
rs2523729	0.81[EUR][1000 genomes]
rs2844777	0.91[EUR][1000 genomes]
rs3094034	0.80[EUR][1000 genomes]
rs3094036	0.80[EUR][1000 genomes]
rs3094054	1.00[EUR][1000 genomes]
rs3094056	1.00[EUR][1000 genomes]
rs3094057	1.00[EUR][1000 genomes]
rs3094058	1.00[EUR][1000 genomes]
rs3094064	0.98[EUR][1000 genomes]
rs3094066	0.95[EUR][1000 genomes]
rs3094067	0.98[EUR][1000 genomes]
rs3094069	0.95[EUR][1000 genomes]
rs3094078	0.95[EUR][1000 genomes]
rs3094620	1.00[EUR][1000 genomes]
rs3094621	0.89[EUR][1000 genomes]
rs3094622	0.89[EUR][1000 genomes]
rs3094624	1.00[EUR][1000 genomes]
rs3094625	1.00[EUR][1000 genomes]
rs3094628	0.90[EUR][1000 genomes]
rs3129815	1.00[EUR][1000 genomes]
rs3129830	0.95[EUR][1000 genomes]
rs3130350	1.00[EUR][1000 genomes]
rs3130351	1.00[EUR][1000 genomes]
rs3130352	1.00[EUR][1000 genomes]
rs3130353	1.00[EUR][1000 genomes]
rs3130355	0.98[EUR][1000 genomes]
rs3130363	0.86[EUR][1000 genomes]
rs3130377	1.00[EUR][1000 genomes]
rs3130380	0.95[EUR][1000 genomes]
rs3130399	0.95[EUR][1000 genomes]
rs3132647	1.00[EUR][1000 genomes]
rs3132648	1.00[EUR][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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130364	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30313400-30321400	Weak transcription	Spleen	Spleen
2	chr6:30313800-30325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:30314000-30319400	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:30314000-30319400	Weak transcription	Colonic Mucosa	Colon
5	chr6:30314000-30323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:30314000-30323200	Weak transcription	Aorta	Aorta
7	chr6:30314000-30324200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:30314000-30325600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:30314200-30322200	Weak transcription	Fetal Brain Male	brain
10	chr6:30314200-30323400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:30314200-30325600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:30314200-30325600	Weak transcription	Psoas Muscle	Psoas
13	chr6:30314400-30319200	Weak transcription	Right Ventricle	heart
14	chr6:30314400-30325000	Weak transcription	Esophagus	oesophagus
15	chr6:30314400-30325400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:30314600-30325600	Weak transcription	Pancreas	Pancrea
17	chr6:30314800-30319400	Weak transcription	NHLF	lung
18	chr6:30315000-30320400	Weak transcription	NHDF-Ad	bronchial
19	chr6:30315000-30323200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:30315000-30323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:30315000-30325600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:30315000-30325600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:30315000-30325600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:30315000-30325600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:30315200-30320400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:30315200-30323200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:30315400-30323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:30315600-30320200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:30315600-30320400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:30315600-30323200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:30315600-30324400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:30315600-30325400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:30315600-30325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:30315800-30324200	Weak transcription	Fetal Intestine Large	intestine
35	chr6:30316000-30325600	Weak transcription	Brain Angular Gyrus	brain
36	chr6:30316200-30319400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:30316200-30319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:30316200-30320600	Weak transcription	Fetal Stomach	stomach
39	chr6:30316200-30322000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:30316200-30324400	Weak transcription	Fetal Intestine Small	intestine
41	chr6:30316200-30325800	Weak transcription	Gastric	stomach
42	chr6:30316600-30324200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:30316800-30320200	Weak transcription	Left Ventricle	heart
44	chr6:30316800-30321000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:30317000-30320000	Weak transcription	Primary T cells from cord blood	blood

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